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

Wed Jan 19 10:22:20 PST 2022

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
>>
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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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