[Vp-integration-subgroup] [Vp-reproduce-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript
Jacob Barhak
jacob.barhak at gmail.com
Wed Feb 23 22:40:22 PST 2022
Thanks Marcella,
Sheriff, James Osborne, Marcella, and James Glazier - please look carefully
since I am making changes related to your affiliation - should eb ok, yet
you should see this.
This is a much better version and there are very few issues that I located
after reading the manuscript. See Below.
I ask that someone with good English grammar knowledge check the list
below:and let me know if there are any problems with my proposed proofs -
especially punctuation and my replacement of :"predict" with "project" - if
there are any objections to any of those edits, I can drop them - except
from 2 major changes in Marcela's State and one typo made in the previous
proofs, all other issues I found may be skipped.
I ask for authors to review sections they wrote and make sure their
affiliation, name, and references are intact.
Unless I have any objections or changes, those proofs will go out to the
Journal within 24 hours to meet the deadline and I will not ask for an
additional round of corrections - so this is the last chance to make edits.
If anyone will want to make edits later, they will be in the form of Errata
which we want to avoid - so please one last push and let us release this
paper to the public.
Hopefully you will approve.
Jacob
####### List of changes ######
Page 1: Lines 78-89 Affiliations need correction and standardization:
2. European Molecular Biology Laboratory, European Bioinformatics Institute
(EMBL-EBI), Cambridge, United Kingdom
should be
Rahuman S. Malik-Sheriff, European Molecular Biology Laboratory, European
Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, UK
Add Hinxton and change Cambridge to Cambridgeshire
3 School of Mathematics and Statistics, University of Melbourne, VIC,
Parkville, Australia
should be
School of Mathematics and Statistics, University of Melbourne, Parkville,
VIC, Australia
Parkville, VIC should be switched in order
12 Department of Mathematics and Computer Science, University of Richmond,
Richmond, CA, United States
should be:
Department of Mathematics and Computer Science, University of Richmond,
Richmond, VA, United States
CA should be VA
17 Biocomplexity Institute, Indiana University, Bloomington, IND, United
States,
should be:
Biocomplexity Institute, Indiana University, Bloomington, IN, United States,
IN Instead of IND since we are using postal abbreviations for all US states
The reference
Cresta, D., Warren, D. C., Quirouette, C., Smith, A. P., Lane, L. C.,
Smith, A. M.,
et al. (2021). Time to Revisit the Endpoint Dilution Assay and to Replace
TCID$_{50}$ and PFU as Measures of a Virus Sample’s Infection
Concentration. arXiv:2101.11526 [q-bio]. Available at: http://arxiv.org/abs/
2101.11526 (Accessed October 24, 2021).
consider changing to:
Cresta, D., Warren, D. C., Quirouette, C., Smith, A. P., Lane, L. C.,
Smith, A. M.,
et al. (2021). Time to Revisit the Endpoint Dilution Assay and to Replace
TCID50 and PFU as Measures of a Virus Sample’s Infection
Concentration. arXiv:2101.11526 [q-bio]. Available at: http://arxiv.org/abs/
2101.11526 (Accessed October 24, 2021).
TCID$_{50}$ should be subscript fro the number - yet if not allowed in a
reference, the $_{} may be better removed
Page 5 - Line 566
fullfills
should be
fulfills
There are 3 l's the last occurrence double l not 4. Apologies 0 this was a
mistake in the last proofs we provided. Please spell check the word and use
the American English version.
page 2 - Line 119
Please replace "predictions" with "forecasts"
Page 3 - Line 306
Please consider instead of
"Therefore we address many issues at lower..."
consider:
"Therefore, we address many issues at lower..."
We ask to consider adding comma after "Therefore" so
Page 3:
Line 341, 342, please replace hyphens with large hyphens with spaces around
them - the hyphens should have been a perpetrator not a connector between
words: i.e.
"
The “promise of
modeling” should be fulfilled already, yet we find modelers
consistently unable to reproduce basic steps–thus stagnating
instead of innovating, or even worse–backtracking progress.
"
should become:
"
The promise of
modeling” should be fulfilled already, yet we find modelers
consistently unable to reproduce basic steps - thus stagnating
instead of innovating, or even worse - backtracking progress.
"
Alternatively, if preferred. just replaces the hyphens with commas to
create the separation
Page 4 line 401 -
Again the hyphen represents separation, so please add spaces around them
and use a large hyphen. So that
"not approved and tested for the anticipated use–because of the"
becomes:
"not approved and tested for the anticipated use - because of the"
alternatively replace with commas around the hyphen to indicate separation
instead of the hyphens
Page 5 line 519 -
Again, hyphens are supposed to separate no connect here. i.e.:
"
While guidelines and concepts of how to establish credibility
of models–even for critical applications–do exist, the field is still
"
should become
"
While guidelines and concepts of how to establish credibility
of models, even for critical applications - do exist, the field is still
"
Please use a large hyphen or alternatively use commas instead of the hyphens
Page 6 line 681:
Please replace:
"predictions" with "projections"
Page 7 line 786
"
Fortunately there are standardization efforts among
languages.
"
should be
"
Fortunately, there are standardization efforts among
languages.
"
Thus adding a comma.
Page 8 line 868-869
Please link this citation to the first reference in the references list:
"(About using a multi-scale mortality model in
the ensemble, Online)"
It is a link to a discussion - if needed remove the word online at the end
- yet this is a reference and not just a comment in parenthesis
Page 9 line 922:
please add spaces around the large hyphen
"
Sometimes models are used (and published) without
specifying the units used for simulation parameters—this is a
practice that needs to be corrected.
"
should be:
Sometimes models are used (and published) without
specifying the units used for simulation parameters — this is a
practice that needs to be corrected.
Alternatively use a comma instead - the hyphen is intended for explanation
separating sentences, not connecting words.
On Wed, Feb 23, 2022 at 8:37 AM Torres, Marcella <mtorres at richmond.edu>
wrote:
> Hello all,
>
> The new, (and final?) proof is attached. At this point I assume we are not
> requesting additional proofs and any remaining minor issues will be
> submitted as comments that the typesetters can easily address? For example,
> for my incorrect affiliation state I would accept and submit comment:
>
> "The affiliation location state for Marcella Torres is incorrect (it
> should be Virginia (VA) rather than California (CA) and should read
> "Department of Mathematics and Computer Science, University of Richmond,
> Richmond, VA, United States""
>
> It looks like the other issues raised with names and affiliations have
> been corrected!
>
> 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:* Jacob Barhak <jacob.barhak at gmail.com>
> *Sent:* Monday, February 14, 2022 9:14 PM
> *To:* Torres, Marcella <mtorres at richmond.edu>
> *Cc:* Rahuman Sheriff <sheriff at ebi.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,
>
> 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
>
>
>
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