[Vp-reproduce-subgroup] [Vp-integration-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript
Alexander Kulesza
alexander.kulesza at novadiscovery.com
Tue Feb 15 00:09:51 PST 2022
Dear all,
URGENT
Did I miss something or is Jonathan Karr simply missing in the author's
list
[image: image.png]
Eric Forgoston is double in the proof!
Best
On Tue, 15 Feb 2022 at 03:14, Jacob Barhak <jacob.barhak at gmail.com> wrote:
> Thanks Marcella,
>
> This one missed me. And I did go over all of the author affiliations, yet
> for some reason I missed this.
>
> I asked for another author's proofs - I assumed that with so many issues,
> there will be a need for another proof.
>
> Once they issue another proof, I will include a correction for this issue.
>
> Hopefully it's the last one.
>
> Jacob
>
>
>
>
>
> On Mon, Feb 14, 2022 at 2:14 PM Torres, Marcella <mtorres at richmond.edu>
> wrote:
>
>> There is a typo in my affiliation location: it should read "Richmond, VA"
>> not "Richmond, CA".
>>
>> I am happy to collect and comments and post them if you still cannot
>> access, Jacob.
>>
>> Marcella
>>
>> 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 Rahuman
>> Sheriff <sheriff at ebi.ac.uk>
>> *Sent:* Saturday, February 12, 2022 1:38 PM
>> *To:* Jacob Barhak <jacob.barhak 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>; John Gennari <gennari at uw.edu>
>> *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.
>>
>> Dear Jacob and all,
>> Please find the proof attached.
>> There are issue that needs attention,
>> for e.g. Jonathan’s name is missing from the authors list.
>>
>> Quick corrections from my side:
>>
>> My last name: Malik-Sheriff
>>
>> Citation: Malik-Sheriff RS
>>
>> In the acknowledgement, please change RS -> Rahuman S. Malik Sheriff, to
>> keep it consistent as you have it for Jonathan Karr.
>>
>> I will read the proof carefully again and report if I find any typos or
>> so. Others can do that too.
>>
>> Best regards
>> Sheriff
>>
>>
>>
>>
>>
>> On 12 Feb 2022, at 18:30, Jacob Barhak <jacob.barhak at gmail.com> wrote:
>>
>> Hi Marcella,
>>
>> The link you sent brings back my own loop profile - not the article - I
>> tried multiple times - and I did not get such correspondence myself. So I
>> am confused as well.
>>
>> If the intention is to update your loop profile, I did this just now.
>>
>> Hopefully this was the request from the publisher. If you see some other
>> proof document, please provide additional details so we can all respond
>> properly.
>>
>> Jacob
>>
>>
>>
>> On Sat, Feb 12, 2022 at 4:46 AM William Waites <wwaites at ieee.org> wrote:
>>
>> I am disturbed that it’s asking me to log in with facebook, linkedin or
>> twitter…
>>
>> > On 11 Feb 2022, at 22:29, Torres, Marcella <mtorres at richmond.edu>
>> wrote:
>> >
>> > Proof available for viewing/acceptance below. We are asked to check it
>> and respond within 48 hours:
>> >
>> > Dear Marcella Torres,
>> >
>> > Systems Biology Production Office has sent you a message. Please click
>> 'Reply' to send a direct response
>> >
>> > I just finished preparing the proof of your article "Model Integration
>> in Computational Biology: the Role of Reproducibility, Credibility and
>> Utility", DOI: 10.3389/fsysb.2022.822606. Could you please check it within
>> 48 hours (excluding weekends and holidays). Make sure to respond in the
>> system so that I'm notified of your corrections.
>> >
>> > Here's the link:
>> >
>> http://www.frontiersin.org/Production/EnterProductionForum.aspx?activationno=886b0bc9-5221-44e7-9475-1aa44986adb5&pagekey=POF_DISCUSSION_FORUM
>> >
>> > P.S. We would recommend that you assign one author to collect all
>> changes and to upload the revised files.
>> >
>> > Do you need help? Visit our Production Help Center for more
>> information:
>> https://zendesk.frontiersin.org/hc/en-us/categories/200397292-Article-Production-
>> >
>> > Best regards,
>> >
>> > Frontiers in Systems Biology Production Office
>> > systemsbiology.production.office at frontiersin.org
>> > www.frontiersin.org
>> >
>> > For technical issues, please contact Application Support -
>> support at frontiersin.org
>> >
>> > ***********
>> > Do you need help?
>> >
>> > -You need to be logged in to your account to access the proof.
>> > -the PDF proof is available in the top right corner, follow the
>> instructions on the PDF to submit your corrections.
>> > -If your article is not linked to your account contact
>> 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: Jacob Barhak <jacob.barhak at gmail.com>
>> > Sent: Friday, February 4, 2022 8:28 PM
>> > To: Torres, Marcella <mtorres at richmond.edu>
>> > Cc: Ruth Bowness <rb2250 at bath.ac.uk>;
>> 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>; John Gennari <gennari at uw.edu>
>> > 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.
>> >
>> > 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
>> ).
>> >
>> > The title, abstract and author(s) list you provided during submission
>> is currently online and will be replaced with the final version when your
>> article is published. Please do not communicate any changes until you
>> receive your proofs.
>> >
>> > Any questions? Please visit our Production Help Center page for more
>> information:
>> https://zendesk.frontiersin.org/hc/en-us/categories/200397292-Article-Production-
>> >
>> > 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
>> >
>> > You can click here to access the final review reports and manuscript:
>> http://www.frontiersin.org/Review/EnterReviewForum.aspx?activationno=176c11a6-62ac-48cd-bc10-66fd193d8aba
>> >
>> > As an author, it is important that you keep your Frontiers research
>> network (Loop) profile up to date, so that you and your publications are
>> more discoverable. You can update your profile pages (profile picture,
>> short bio, list of publications) using this link:
>> https://loop.frontiersin.org/people/
>> >
>> > ------------------
>> > Tell us what you think!
>> >
>> > At Frontiers we are constantly trying to improve our Collaborative
>> Review process and would like to get your feedback on how we did. Please
>> complete our short 3-minute survey and we will donate $1 to Enfants du
>> Monde, a Swiss non-profit organization:
>> >
>> https://frontiers.qualtrics.com/jfe/form/SV_8q8kYmXRvxBH5at?survey=author&aid=822606&uid=1393232
>> >
>> > Thank you very much for taking the time to share your thoughts.
>> >
>> > Best regards,
>> >
>> > Your Frontiers in Systems Biology team
>> >
>> > Frontiers in Systems Biology Editorial Office
>> > www.frontiersin.org
>> > 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: 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
>> > Twitter: @RuthBowness
>> >
>> > 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.
>> >
>> > <image001.jpg>
>> >
>> >
>> >
>> >
>> >
>> > 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
>> >
>> > 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
>> > 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
>> > _______________________________________________
>> > Vp-integration-subgroup mailing list
>> > Vp-integration-subgroup at lists.simtk.org
>> > https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
>>
>> _______________________________________________
>> Vp-reproduce-subgroup mailing list
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>>
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> Vp-integration-subgroup at lists.simtk.org
> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
>
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Alexander Kulesza
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alexander.kulesza at novadiscovery.com
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