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

Thu Dec 16 17:56:32 PST 2021

Hi all,

Just checking in: am I the only one seeing the reviewer's comments on the manuscript?

Thanks,
Marcella

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: Monday, November 29, 2021 2:39 AM
To: James A Glazier <jaglazier at gmail.com>
Cc: Thompson, Robin <Robin.N.Thompson at warwick.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>; Jonathan Karr <jonrkarr at gmail.com>; John Gennari <gennari at uw.edu>; Winston Garira <Winston.Garira at univen.ac.za>; Faeder, James R <faeder at pitt.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 James, And thanks to all contributors,

The paper was submitted on Thanksgiving evening and confirmation was received.

Hopefully it will be processed quickly.

          Jacob

On Wed, Nov 24, 2021 at 12:22 PM James A Glazier <jaglazier at gmail.com<mailto:jaglazier at gmail.com>> wrote:

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<mailto: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<mailto:jacob.barhak at gmail.com>>
Date: Wednesday, November 24, 2021 at 6:47 AM
To: John Rice <john.rice at noboxes.org<mailto:john.rice at noboxes.org>>, Jonathan Karr <jonrkarr at gmail.com<mailto:jonrkarr at gmail.com>>, William Waites <wwaites at ieee.org<mailto:wwaites at ieee.org>>, Tingting Tang <ttang2 at sdsu.edu<mailto:ttang2 at sdsu.edu>>, vp-reproduce-subgroup at lists.simtk.org<mailto:vp-reproduce-subgroup at lists.simtk.org> <vp-reproduce-subgroup at lists.simtk.org<mailto:vp-reproduce-subgroup at lists.simtk.org>>, James A Glazier <jaglazier at gmail.com<mailto:jaglazier at gmail.com>>, vp-integration-subgroup at lists.simtk.org<mailto:vp-integration-subgroup at lists.simtk.org> <vp-integration-subgroup at lists.simtk.org<mailto:vp-integration-subgroup at lists.simtk.org>>, John Gennari <gennari at uw.edu<mailto:gennari at uw.edu>>, Winston Garira <Winston.Garira at univen.ac.za<mailto:Winston.Garira at univen.ac.za>>, Faeder, James R <faeder at pitt.edu<mailto:faeder at pitt.edu>>, Thompson, Robin <Robin.N.Thompson at warwick.ac.uk<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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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