[Vp-reproduce-subgroup] [Vp-integration-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript
Jacob Barhak
jacob.barhak at gmail.com
Mon Feb 14 18:14:12 PST 2022
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
> Vp-reproduce-subgroup at lists.simtk.org
> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.simtk.org/pipermail/vp-reproduce-subgroup/attachments/20220214/0247b0b6/attachment-0001.html>
More information about the Vp-reproduce-subgroup
mailing list