[Vp-integration-subgroup] [Vp-reproduce-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript
William Waites
wwaites at ieee.org
Sun Feb 13 07:33:58 PST 2022
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
>
>
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>
>> 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 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>
>>
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