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

Wed Nov 24 06:14:03 PST 2021

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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