[Vp-reproduce-subgroup] [Vp-integration-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript
Tingting Tang
ttang2 at sdsu.edu
Sun Feb 13 08:32:59 PST 2022
Hi, Jacob,
I have completed registration to frontier site.
Thanks very much for your leading efforts in publishing this work!
Best,
Tingting
On Sun, Feb 13, 2022 at 7:34 AM William Waites <wwaites at ieee.org> wrote:
> Jacob, my affiliation is hopelessly mangled. It interleaved department
> names at two universities. I am not near a computer so I cannot fix it now.
>
> On 13 Feb 2022, at 15:01, Jacob Barhak <jacob.barhak at gmail.com> wrote:
>
>
> Thanks Marcella, Also thanks to Sheriff, William, Eric, and Gilberto,
>
> With your help I was able to complete the proofs/
>
> You will find a link to the proofs document here:
>
>
> https://drive.google.com/file/d/1PmRotuMlNN-plR524JhxrtAIc857zIF1/view?usp=sharing
>
> I uploaded the proofs to the system - it seems to work now and I am able
> to access the production portal.
>
> I requested another round of proofs - just to make sure all our requests
> were handled correctly.
>
> Below is the text of the proofs to make things more readable - the
> proofs are per question.
>
> Jonathan, please make sure your name and affiliation are corrected.
>
> Eric, John,TingTing, William, James, Q6 asked you to.register with
> Frontiers at https://www.frontiersin.org/
> Registration/Register.aspx - this way it can display your profiles. It
> may provide other services.
>
> William, please follow my request.
>
> Hana, Wiliam, Eric there were discrepancies with some of your references -
> I did my best to resolve that, yet please make sure I did not make any
> mistake in those - the changes you made late introduced some problems -
> please check my responses and sections you contributed to.
>
> Sheriff, just noticed that one of your proofs may introduce a typo -
> "fullfills" - I hope they will catch it - otherwise we will need to repeat
> the process.
>
> Many thanks to you all.
>
> And I hope this will be the last proof round.
>
>
> Jacob
>
>
>
>
>
> ######### Proofs sent per question #############
>
>
> Q1: Running title is ok
>
> Q2: If possible, please separate at colon into different lines, try to
> keep "computational Biology" on the same line
>
> Q3: There is a discrepancy in the author list in the version sent to us.
> The correct author names and affiliation is provided in our draft:
> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
> Please use the names and affiliations as provided there - this list was
> approved and corrected by all authors - specifically, there seems to be an
> error with the first author - Eric Forgoston is the 5th author - he is
> repeated twice by mistake as the first author and the 5th author. The first
> author is Jonathan Karr. - please make the correction for the author list
> to match the link above.
>
>
> Q4: Thank you, you did correctly - the names should match this link:
> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>
>
> Q5: The second author surnames has a hyphen. His corrected surname for
> consistency is Malik-Sheriff with a hyphen - the correct version of all
> names is in this link:
> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>
> This list was been reviewed by all authors. and corrected multiple times
>
>
> Q6: this proof will be posted to the mailing list with all authors - the
> specific authors will be notified specifically to register as requested.
>
>
> Q7: The correct affiliations are in this link:
> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>
> Please note that William Waites has 2 affiliations -you did try to fix
> this, yet both affiliations got mixed up to the point that the current
> version is confusing since departments and schools are written in a
> different order. The correct text should be:
>
> William Waites, Centre for Mathematical Modelling of Infectious Diseases,
> London School of Hygiene and Tropical Medicine, London, UK and Department
> of Computer and Information Sciences, University of Strathclyde, Glasgow,
> Scotland
>
>
> Q8: Thanks you - corresponding authors email addresses are correct.
>
>
> Q9: Thank you - keywords are ok
>
>
> Q10: Title leveling is ok - thank you for being observant
>
>
> Q11: the citation should be
> (Stack et. al., 2013) - thank you for being observant - the reference
> exists already - just the citation test should be changed on page 9 line
> 1004
>
>
> Q12: Thank you - the final comments of reviewer 1 were seriously take and
> the submission system contains multiple versions of figures - in multiple
> formats. If this is insufficient we will be happy to provide more versions
> - yet the images look ok in the version even with 400% magnification, so I
> assume this is ok.
>
>
> Q13: Thank you - this is important to explain author contributions. Here
> is exact text to be used:
> "
> All authors listed have made direct, and intellectual contribution to the
> work and approved it for publication. Contributions can be traced back
> using the links in appendix 1. Looking through versions will reveal
> contribution level of authors. Entries listed under the name of the
> corresponding author sometimes represent text from other listed authors
> communicated outside the documents. The group made an effort to keep the
> work as traceable as possible in the spirit of reproducibility.
> "
>
>
> Q14: the topic of funding was discussed by the group multiple times - the
> section you have is correct with one small change - if you are using
> acronyms - please change Jonathan Karr to JK at th beginning to match all
> names - or use the full names for everyone.
>
>
>
> Q15: Thank you - you did well separating acknowledgments form funding
>
>
> Q16: The conflict of interest section is missing. One of the corresponding
> authors reports conflict of interest in the format of "ICMJE Form for
> Disclosure of Potential Conflicts of Interest" . Below is the text again.
> It is better this text be used to avoid any questions later on with regards
> to funding. It is OK to mention AK is employed by Novadiscovery, yet he
> reported no conflict on interest when asked. Nevertheless, its better to
> mention all elements rather than omit by neglect - it is the proper thing
> to do. Here is the full text again with some corrections to reflect changes
> you made in the editors note:
>
> "
> Alexander Kulesza was employed by the Novadiscovery SA.
>
> Dr. Jacob Barhak: Payment/services info: Dr. Barhak reports non-financial
> support and other from Rescale, and MIDAS Network, other from Amazon AWS,
> Microsoft Azure, MIDAS network, other from The COVID tracking project at
> the Atlantic, other from John Rice and Jered Hodges, other from Anaconda.
> Financial relationships: Jacob Barhak declare(s) employment from U.S.
> Bank/Apexon, MacroFab, United Solutions, B. Well Connected health and
> Anaconda. Intellectual property info: Dr. Barhak holds US Patent 9,858,390
> - Reference model for disease progression issued to Jacob Barhak, and a US
> patent 10,923,234 - Analysis and Verification of Models Derived from
> Clinical Trials Data Extracted from a Database. Other relationships: During
> the conduct of the study; personal fees from U.S. Bank/Apexon, personal
> fees from MacroFab, personal fees from United Solutions, personal fees from
> B. Well Connected health, personal fees and non-financial support from
> Anaconda, outside the submitted work.
> "
>
>
>
> Q17: thanks for noticing.
> The Reference "Assaf et al., 2011" is outdated from a previous version and
> can be removed.
>
> Bai et al., 2021 was added with the intention to cite in a late revision,
> yet never properly referenced. It is better to remove it since we neglected
> to reference it - at this point we rather not make any changes to the text
> to add it.
>
> Khain et al., is outdated from a previous version and should be removed.
>
> (Wang et. al., 2019) should be referenced in the following text page 9 -
> line 1007:
> "because it can be shared, it can be used for calibration Q11 and
> validation of other models (Barhak, 2017; Ajelle et al., 2018; Liu et al.,
> 2018; Wang et al., 2019)." instead of Wang et al., 2020. Thanks for
> noticing this.
>
> Stack et al. replaces Bansal et al., 2013 on page 9 line 1004 as
> requested in Q11. The reference in that spot switched author order by
> midtake and shoudl be crrected.
>
>
>
> Q18:
> Reference Cresta et al. is a preprint. It was read from the preprint that
> did nto have DOI. The version in the paper has the following DOI:
> 10.1371/journal.pcbi.1009480
> The preprint has not volume number other than the link we provided.
> I suggest adding the DOI and mentioning that the reference was later made
> available.
>
> as for Sarma et al., 2016. - this is the suggested citation accoding to
> F1000 - it includes a DOI
> Sarma GP, Jacobs TW, Watts MD et al. Unit testing, model validation, and
> biological simulation [version 1; peer review: 2 approved, 1 approved with
> reservations]. F1000Research 2016, 5:1946 (
> https://doi.org/10.12688/f1000research.9315.1)
>
>
>
>
> Q19: Can you please explain the question. Fujimoto et al., 2017.”
> is a book. Here is the link to it:
> https://link.springer.com/book/10.1007/978-3-319-58544-4
>
>
> Q20: The reference is part of a book.
> Page range is:
> pages = {73–86}
>
> Here is additional citation information in BibText format:
>
> @inbook{10.1145/3411497.3420211,
> author = {Garfinkel, Simson L. and Leclerc, Philip},
> title = {Randomness Concerns When Deploying Differential Privacy},
> year = {2020},
> isbn = {9781450380867},
> publisher = {Association for Computing Machinery},
> address = {New York, NY, USA},
> url = {https://doi.org/10.1145/3411497.3420211},
> abstract = {The U.S. Census Bureau is using differential privacy (DP) to
> protect confidential respondent data collected for the 2020 Decennial
> Census of Population & Housing. The Census Bureau's DP system is
> implemented in the Disclosure Avoidance System (DAS) and requires a source
> of random numbers. We estimate that the 2020 Census will require roughly
> 90TB of random bytes to protect the person and household tables. Although
> there are critical differences between cryptography and DP, they have
> similar requirements for randomness. We review the history of random number
> generation on deterministic computers\o{}mitt, including von Neumann's
> "middle-square'' method, Mersenne Twister (MT19937) (the default NumPy
> random number generator, which we conclude is unacceptable for use in
> production privacy-preserving systems), and the Linux /dev/urandom device.
> We also review hardware random number generator schemes, including the use
> of so-called "Lava Lamps'' and the Intel Secure Key RDRAND instruction. We
> finally present our plan for generating random bits in the Amazon Web
> Services (AWS) environment using AES-CTR-DRBG seeded by mixing bits
> from/dev/urandom and the Intel Secure Key RDSEED instruction, a compromise
> of our desire to rely on a trusted hardware implementation, the unease of
> our external reviewers in trusting a hardware-only implementation, and the
> need to generate so many random bits.},
> booktitle = {Proceedings of the 19th Workshop on Privacy in the Electronic
> Society},
> pages = {73–86},
> numpages = {14}
> }:
>
>
>
>
> Q21:
> Hart et al. 2020 is a e preprint that was later published as an e
> publication. There is no page number. The web page provides the following
> citation:
> eLife 2021;10:e65534 DOI: 10.7554/eLife.65534
>
> Hernandez-Vargas and Velasco-Hernandez, 2020 is a preprint. The citation
> information reads:
>
>
> In-host Modelling of COVID-19 in Humans
> Esteban A. Hernandez-Vargas, Jorge X. Velasco-Hernandez
> medRxiv 2020.03.26.20044487; doi:
> https://doi.org/10.1101/2020.03.26.20044487
>
>
> Ke et al., 2020 is a preprint. The citation information reads:
> Kinetics of SARS-CoV-2 infection in the human upper and lower respiratory
> tracts and their relationship with infectiousness
> Ruian Ke, Carolin Zitzmann, Ruy M. Ribeiro, Alan S. Perelson
> medRxiv 2020.09.25.20201772; doi:
> https://doi.org/10.1101/2020.09.25.20201772
>
>
>
> Q22: Figures and tables are correct with correct titles and of sufficient
> quality even when zoomed to.
>
>
> Q23: Thanks - this is an important appendix since it provides traceability
> and the paper discusses credibility and we want to be as open as possible
> and provide an example of how to trace back work back to origin. The
> appendix is now referenced in the text provided in the author contribution
> section. See Q13 above.
>
>
> Q24: Thank you -The appendix is correct. the links correctly lead to
> material that constructed this paper - it is important for us to show the
> history of this paper - this appendix is important.
>
>
> Q25: There is no issue there. The figures and ables were specifically
> created for this article. Rahuman Sheriff created figure 1. Alexander
> Kuesza created figure 2 in response th a reviewers request. Jacob Barhak
> created the table that was later modified by many authors - those are all
> original
>
>
>
>
>
> In addition to these questions, during rereading of the paper we detected
> the following elements that you may wish to correct to keep consistency and
> use American English:
>
> Page 2 - line 211: catalogue -> catalog
> Page 2 - line 213: catalogues -> catalogs
> Page 3 - line 313: behaviour -> behavior
> Page 3 - line 314: Afterall -> After all,
> Page 4 - line 363: catalogued -> cataloged
> Page 4 - line 415: risk adjusted -> risk-adjusted
> Page 4 - line 453: physics driven -> physics-driven
> Page 4 - line 470: model informed -> model-informed
> Page 5 - line 569: fulfils-> fullfills
> Page 7 - line 767: matlab -> MATLAB
> Page 8 - line 846: matlab -> MATLAB
> Page 10 - line 1087: Real world -> Real-world
> Page 11 - line 1216: Real world -> Real-world
> Page 12 - line 1349: non technical -> non-technical
>
>
>
>
>
>
>
>
>
> On Sun, Feb 13, 2022 at 2:20 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
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>> > >
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>> > >
>> > > 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
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>> > >
>> > > 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>
>>
>>
--
Tingting Tang
Assistant Professor
San Diego State University Imperial Valley
Office: FOBE 110
Phone: 760-768-5531
720 Heber Ave
Calexico, CA 92231
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