[Vp-reproduce-subgroup] [Vp-integration-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript

James A Glazier jaglazier at gmail.com
Wed Nov 24 10:22:34 PST 2021


Dear Jacob:

Thank you for all your hard work and patience on this paper. I know you 
have made a lot of effort to integrate so many differing ideas and voices.

JAG

On 11/24/2021 9:14 AM, Jacob Barhak wrote:
> Thanks James,
>
> Unless there are any last minute objections, I will submit the paper 
> this holiday weekend.
>
> I will update you all on progress.
>
> Hopefully it will be smooth.
>
> Happy thanksgiving.
>
>            Jacob
>
> On Wed, Nov 24, 2021 at 8:09 AM Faeder, James R <faeder at pitt.edu> wrote:
>
>     APPROVE. I apologize for the delay. These messages were being
>     routed to a folder that I do not check frequently. I finally found
>     out from a voicemail message. Thanks everyone for the efforts you
>     have put into this work and especially Jacob for all of the work
>     organizing on top of it. Good luck with the submission and Happy
>     Thanksgiving!
>
>     Jim
>
>     *From: *Jacob Barhak <jacob.barhak at gmail.com>
>     *Date: *Wednesday, November 24, 2021 at 6:47 AM
>     *To: *John Rice <john.rice at noboxes.org>, Jonathan Karr
>     <jonrkarr at gmail.com>, William Waites <wwaites at ieee.org>, Tingting
>     Tang <ttang2 at sdsu.edu>, vp-reproduce-subgroup at lists.simtk.org
>     <vp-reproduce-subgroup at lists.simtk.org>, James A Glazier
>     <jaglazier at gmail.com>, vp-integration-subgroup at lists.simtk.org
>     <vp-integration-subgroup at lists.simtk.org>, John Gennari
>     <gennari at uw.edu>, Winston Garira <Winston.Garira at univen.ac.za>,
>     Faeder, James R <faeder at pitt.edu>, Thompson, Robin
>     <Robin.N.Thompson at warwick.ac.uk>
>     *Subject: *Re: [Vp-integration-subgroup] [Vp-reproduce-subgroup]
>     Shayn Peirce-Cottler via Frontiers: Manuscript
>
>     Greetings James Faeder,
>
>     You are the last one that needs to Approve. DISAPPROVE , or
>     ABSTAIN from submission of the paper.
>
>     I apologize if you already sent a response yet I have not located
>     any response from you- it may be my error, yet I need your public
>     response before I can continue to submit the paper.
>
>     17 of us already approved submission and you are the last one on
>     my list.
>
>     I tried to contact your department in the last few days and left
>     voice messages to your administrators since I could not locate
>     your direct phone.
>
>     I will really appreciate it if someone can contact you and make
>     sure you get this message.
>
>     I really hope we get an answer so I can process the paper by
>     thanksgiving weekend.
>
>                       Jacob
>
>     On Fri, Nov 19, 2021 at 12:22 AM Jacob Barhak
>     <jacob.barhak at gmail.com> wrote:
>
>         Thanks John, Hi James Faedar,
>
>         John, with your approval below we only need James Faedar to
>         respond so I can proceed.
>
>         Can someone contact him to make sure he saw this
>         correspondence? He should receive these messages, yet if
>         someone is in contact with him regularly, please ask him to
>         respond so we can move on.
>
>         One last thing before submission. If there is anyone who
>         thinks this paper should not be published, I would ask them to
>         write to this mailing list publicly - if there is any error or
>         omission that anyone thinks is important, we want to know
>         about it before submitting the article. This request is public
>         and not targeted at the authors - if there is something we
>         missed, we want to know it before submission.
>
>         Hopefully James Feedar will respond quickly and there will be
>         no public objection and we can get this paper published quickly.
>
>                       Jacob
>
>         On Thu, Nov 18, 2021 at 4:34 PM John Rice
>         <john.rice at noboxes.org> wrote:
>
>             I approve submission.
>
>             Typed with two thumbs on my iPhone.  (757) 318-0671
>
>             “Upon this gifted age, in its dark hour,
>
>             Rains from the sky a meteoric shower
>
>             Of facts . . . they lie unquestioned, uncombined.
>
>             Wisdom enough to leech us of our ill
>
>             Is daily spun; but there exists no loom
>
>             To weave it into fabric.”
>
>             –Edna St. Vincent Millay,
>
>
>             On Nov 17, 2021, at 22:04, Jacob Barhak
>             <jacob.barhak at gmail.com> 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
>
>                             _______________________________________________
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>                             Vp-integration-subgroup at lists.simtk.org
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>
-- 
James A. Glazier, PhD
Professor of Intelligent Systems Engineering, Adjunct Professor of Physics
Director, Biocomplexity Institute
Indiana University, Bloomington
(812) 391-2159 (cell)
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