[Vp-reproduce-subgroup] [Vp-integration-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript
Yaling Liu
yal310 at lehigh.edu
Sun Feb 13 17:28:02 PST 2022
Jacob,
Thanks for the detailed explanation. Sure, I am totally fine with
whichever makes things easier.
You obviously contributed a lot on the software development and unit
standardization and deserve some payback. I have been pushing development
of some cloud-based software for hemolysis prediction for the past year -
it is so painful even with the support of NIH, so I can understand your
efforts.
Let's help promote this paper by sharing on social media....I'll at least
post it on my twitter this week.
Yaling
On Sun, Feb 13, 2022 at 4:05 PM Jacob Barhak <jacob.barhak at gmail.com> wrote:
> Thanks Yaling,
>
> If you insist I do more paperwork than necessary I can reluctantly get
> reimbursed. However, I would rather avoid it if you don't mind. because:
>
> 1. I am considered a business and this expense is tax deductible
> 2. The amount of time it will take me to process 17 requests with
> different institutions will just add more paperwork to the point that it is
> not worthwhile my time - I value my time so I ask that you do not force me
> to spend it on mindless paperwork multiplied many times for many authors. I
> am not getting paid for doing such extra paperwork.
> 3. Most of us are volunteers and were not expecting to pay anything - I
> rather keep it that way - if those who are funded to do this work
> would have covered the costs - it would have been a different matter - yet
> I rather keep the volunteers not paying and they may feel compelled to do
> so if we start this.
> 4. I do have a conflict of interest declared. I have interest in the
> recommendations in our paper being implemented - it is worth a lot of money
> for me if some of those elements are adopted. I invested almost all of my
> life savings in modeling technology in the last decade and I intend to
> profit from it - compared to potential profits this publication cost is
> negligible.
>
> The last point is the most important one and to be transparent I
> should elaborate. There are two sections that are very important for my own
> future - Licensing and Unit standardization.
>
> With regards to licensing, I can tell you that during the pandemic I was
> blocked multiple times on licensing issues. Eric saw some communications on
> the matter in some minor cases, yet it goes further with regards to
> software licensing that does not provide incentive for innovation. I
> attempted to change things multiple times and was faced with entities
> attempting to ignore me or not engage in discussion, or entities that were
> actually taking an opposing position - some of those conversations were
> reported in the paper so I rather keep private, yet some of those blocks
> related to licensing substantially diminish my capability to innovate. In
> this group of authors I got support from many and this may be what is
> needed to change the direction things were going in. I can be more
> specific, yet I rather not get into finger pointing and leave this
> explanation as is. If you want additional information I can provide it, yet
> I rather keep it at a non personal level of discussion.
>
> As for the unit standardization, I have a project that I am trying to
> monetize: https://clinicalunitmapping.com/about
> This is an essential component in many solutions in future modeling - this
> problem prevents us from being able to computational model things because
> what I call the Tower of Babel effect - where each data arrives in a
> different language = unit - making it impractical to integrate data and
> models. This publication may be necessary to boost interest in this project
> that is very important for many applications beyond modeling. And I do have
> claims in my latest patent related to this project. So I do want to
> accelerate the process by publishing this fast - this is why I paid the fee
> willingly.
>
> If you want to help, I would rather you look at the publications and
> videos in the project website above and propagate it in your community - it
> is worth much more than reimbursing me for publication costs.
>
> Another important topic that some of us were discussing is
> model combination - I have 2 US patents on this technology that I wish to
> license - so this paper helps in that direction - it is good advertising -
> especially since so many people from diverse institutions are signed on to
> it.
>
> You see, I have an incentive to move things forward quickly in the field
> of computational biological modeling and I believe I will be reimbursed
> properly with substantial profit - I left the academic system to do this
> years ago since I could not advance things as fast within the system. This
> is why I spent so much time on this paper - it aligns with my interests
> both intellectually and financially.
>
> I hope my explanation is sufficient to prevent more such requests to share
> payment - if you want to help, please take time to look at my publication
> and if you want to collaborate - you can pick up the costs of the next
> paper ... I think it's a fair bargain.
>
> Jacob
>
>
> On Sun, Feb 13, 2022 at 10:59 AM Yaling Liu <yal310 at lehigh.edu> wrote:
>
>> Jacob,
>>
>> The proof looks good to me.
>> Thanks for leading this great effort!
>>
>> I would like to contribute to part of the publication cost too if you can
>> tell me the split of the cost and share the receipt.
>>
>> Thanks.
>>
>> Yaling
>>
>> On Sun, Feb 13, 2022 at 3:31 AM William Waites <wwaites at ieee.org> wrote:
>>
>>> My affiliation is pretty amusingly mangled
>>>
>>> > On 13 Feb 2022, at 02:50, Torres, Marcella <mtorres at richmond.edu>
>>> wrote:
>>> >
>>> > That's unfortunate; attached is the proof document. Here is the text
>>> that accompanies the proof:
>>> >
>>> > Here you can view and reply to the comments of the typesetter, who
>>> produces the Author’s Proof. Your replies and eventual further comments
>>> will be incorporated into the final article production.
>>> >
>>> > When you are finished with replying to comments, please make sure to
>>> ”Post comments” in order to inform the typesetter of your replies/comments
>>> and to indicate if you need to see another Author’s Proof or not.
>>> >
>>> > Please note: Requesting another Author’s Proof prolongs the production
>>> process significantly. You should ONLY request to see another proof if you
>>> made major changes to formulas, figures or tables. Any other changes can be
>>> easily incorporated into the final article production and you should
>>> approve the proof.
>>> >
>>> > Here are the options we can choose from after reviewing the proof:
>>> > <image.png>
>>> > 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: Saturday, February 12, 2022 1:30 PM
>>> > To: William Waites <wwaites at ieee.org>
>>> > Cc: Torres, Marcella <mtorres at richmond.edu>;
>>> 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-integration-subgroup] [Vp-reproduce-subgroup] Shayn
>>> Peirce-Cottler via Frontiers: Manuscript
>>> >
>>> > External Email: Use caution in opening links, attachments, and buying
>>> gift cards.
>>> >
>>> > 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
>>> >
>>> > <Author's Proof.pdf>
>>>
>>> _______________________________________________
>>> Vp-integration-subgroup mailing list
>>> Vp-integration-subgroup at lists.simtk.org
>>> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
>>>
>>
>>
>> --
>> -- ------------------
>> Yaling Liu, Professor
>> Department of Bioengineering, Director of Graduate Studies
>> Department of Mechanical Engineering and Mechanics
>> Lehigh University
>> www.lehigh.edu/~yal310
>> _______________________________________________
>> Vp-reproduce-subgroup mailing list
>> Vp-reproduce-subgroup at lists.simtk.org
>> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>>
>
--
-- ------------------
Yaling Liu, Professor
Department of Bioengineering, Director of Graduate Studies
Department of Mechanical Engineering and Mechanics
Lehigh University
www.lehigh.edu/~yal310
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