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

[Jacob Barhak]

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 should not be published, I would ask them to write to this mailing list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
>>>
>>> _______________________________________________
>>> Vp-integration-subgroup mailing list
>>> Vp-integration-subgroup at lists.simtk.org
>>> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
>>>
>>>
>>>
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