[Vp-integration-subgroup] [Vp-reproduce-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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>
--
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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