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

Wed Jan 19 10:26:20 PST 2022

Jacob, I don’t think this is a big deal. This kind of non-substantive change should be possible (e.g. when we get the proofs and any missing dots and crosses on t’s and I’s are checked)

> On 19 Jan 2022, at 18:22, Jacob Barhak <jacob.barhak at gmail.com> wrote:
> 
> 
> 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
>>>>> 
>>>>> _______________________________________________
>>>>> Vp-integration-subgroup mailing list
>>>>> Vp-integration-subgroup at lists.simtk.org
>>>>> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
>>>> 
>> -- 
>> 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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