[Vp-reproduce-subgroup] White paper revision

John Gennari gennari at uw.edu
Fri May 14 14:48:26 PDT 2021


Potential co-authors:

As promised, attached find the skeleton of a complete re-writing and 
revision of the white paper. This new version is tentatively titled "A 
dozen challenges to biosimulation model reproducibility and 
integration", reflecting a new focus to the paper.

I have also placed this document on a shared drive, where all of you 
have the ability to comment (not edit): 
https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit 
(I hope I've done the settings correctly! Let me know if not.)

It's important to note that this new draft is just a skeleton, and not a 
complete paper yet. I have provided a new introduction based on Fig 1 
and Table 1 as I suggested in my earlier email. I have not yet adapted 
or modified any of the 12 subsections that correspond to the 12 
challenges. This is work that could be distributed among co-authors, of 
course.

I also have not yet created any good organization of these 12 
challenges, although I put in one idea (in yellow, at the end). Others 
would be very welcome.

Although I think this provides a much stronger organization to the 
paper, I'm aiming to nonetheless be faithful to the central ideas of the 
earlier draft, and thus I view it as a revision, rather than a 
completely new paper.

My main goal for disseminating the attached is to get feedback -- is 
this a reasonable direction to head in for the revision? Are there 
critical elements or ideas that I'm missing from the introduction? As 
you can see below, Eric has kindly set up a "whenisgood" poll for a 
potential meeting on Monday or Tuesday (5/17 or 5/18). Eric, please let 
us know if we have a quorum for any particular time. (The earlier you 
can let us know, the better!)

Of course, if you aren't available to chat on Mon/Tues, email comments 
and discussion are welcome!

-John Gennari


On 5/12/2021 8:04 PM, Eric Forgoston wrote:
> Here is a link to a meeting poll for next Monday/Tuesday, 17/18 May. 
> Please fill out by Friday, 14 May, so we can set a day/time to discuss 
> the revision.
>
> http://whenisgood.net/kdrzmkj <https://whenisgood.net/kdrzmkj>
>
> Cheers,
>
> Eric
> ---------------------
> Dr. Eric Forgoston
> Professor of Applied Mathematics
> Chair, Department of Applied Mathematics and Statistics
> Montclair State University
> Montclair, NJ  07043 USA
> +1 973 655-7242
> https://eric-forgoston.github.io/ <https://eric-forgoston.github.io/>
>
>
> On Wed, May 12, 2021 at 2:09 PM John Gennari <gennari at uw.edu 
> <mailto:gennari at uw.edu>> wrote:
>
>
>     This is definitely a good idea. The challenge might be to schedule
>     a time when a sufficient quorum of us are available....
>
>     My plan over the rest of this week is to draft up a significant
>     re-working of the paper, and then distribute that to all. This
>     won't be a complete revision, but rather some example of the kinds
>     of things to say, and some outlines of the proposed
>     re-organization. I should have this done by Friday, or this
>     weekend at the latest. So then a Zoom call next week (Monday, May
>     17?) might make sense to talk thru the ideas that I send out by
>     this Friday.
>
>     -John G.
>
>
>     On 5/11/2021 7:37 PM, Eric Forgoston wrote:
>>     Dear all,
>>
>>     It is probably worth having a zoom chat to discuss the revision
>>     so that we are all working in concert.  In particular, John
>>     Gennari sent an email last week on May 3 with some thoughts that
>>     are well-worth discussing.
>>
>>     Is there interest in doing this?
>>
>>     Cheers,
>>
>>     Eric
>>     ---------------------
>>     Dr. Eric Forgoston
>>     Professor of Applied Mathematics
>>     Chair, Department of Applied Mathematics and Statistics
>>     Montclair State University
>>     Montclair, NJ 07043 USA
>>     +1 973 655-7242
>>     https://eric-forgoston.github.io/ <https://eric-forgoston.github.io/>
>>
>>
>>     On Tue, May 11, 2021 at 10:26 AM Jacob Barhak
>>     <jacob.barhak at gmail.com <mailto:jacob.barhak at gmail.com>> wrote:
>>
>>         Greetings white paper contributors,
>>
>>         The voting period is over and the vote did not change, so it
>>         is now time to act.
>>
>>         The paper will be revised as requested by 10 voters and the
>>         target journal will be Bioinformatics - James Glazier and
>>         Yaling Liu will share publication costs.
>>
>>         All those who asked to revise are requested to make the
>>         revisions and discuss those.
>>
>>         I ask to reach a revised version by May 25 so that we can
>>         finish an approval round by June 1st.
>>
>>         So far only Sheriff provided suggestions for revisions prior
>>         to submission so I suggest we start discussing those:
>>         https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit
>>         <https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit>
>>
>>         However, since it is out of format and out of date, I
>>         suggest that all those who want to make changes login and
>>         request to access the main document and introduce changes there:
>>         https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>>         <https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing>
>>
>>         I do ask that this will not be delayed any further and those
>>         who asked for changes give this task priority so it can be
>>         completed in time.
>>
>>         I look forward to your contributions.
>>
>>                     Jacob
>>
>>
>>         On Sun, May 9, 2021 at 4:25 PM Jacob Barhak
>>         <jacob.barhak at gmail.com <mailto:jacob.barhak at gmail.com>> wrote:
>>
>>             Greetings white paper contributors,
>>
>>             Allow me to remind you that the Voting and vote changes
>>             are still possible until 11-May 1am CDT
>>
>>             The current votes I saw are:
>>
>>             10 votes for revision
>>             Jonathan Karr
>>             Eric Forgoston
>>             William Waites
>>             James Glazier  - RS Interface or Bioinformatics
>>             Rahuman Sheriff
>>             Yaling Liu - Bioinformatics
>>             John Rice
>>             Winston Garira
>>             Gilberto Gonzalez-Parra
>>             James Osborne
>>
>>             It seems 2 people supported Bioinformatics - James
>>             Glazier and Yaling Liu  so if this vote is accepted, they
>>             will split publication costs and the terget venue for
>>             revisions will be Bioinformatics.
>>
>>             There is currently 1 minority vote:
>>             Jacob Barhak for direct submission to Nature -
>>              Scientific Reports
>>
>>             If revision is selected, time will be limited, so I
>>             suggest those who voted to start working on revisions.
>>
>>             Hopefully this reminder will move us forward.
>>
>>                         Jacob
>>
>>
>>
>>             On Sat, May 1, 2021 at 12:18 PM Jacob Barhak
>>             <jacob.barhak at gmail.com <mailto:jacob.barhak at gmail.com>>
>>             wrote:
>>
>>                 Greetings white paper contributors,
>>
>>                 It is time to vote again for the target venue. Here
>>                 are the options again.
>>
>>                  1. Cureus - resubmission after addressing editor
>>                     comments
>>                  2. Nature - if you vote for this venue please
>>                     specify flavour such as Nature Scientific Reports
>>                  3. Science
>>                  4. Briefings in Bioinformatics
>>                  5. Trends in Biotechnology - requires distilling the
>>                     paper
>>                  6. Journal of The Royal Society Interface
>>                  7. Annual Review of Public Health
>>                  8. BMJ
>>                  9. Annual Review of Biomedical Engineering
>>                 10. F1000research - if you vote for this this venue
>>                     please specify Gateway / Collection
>>                 11. bulletin of mathematical biology
>>                 12. Bioinformatics.
>>                 13. Do not submit now - instead open for revisions
>>                     for 2 weeks and then submit. If you choose this
>>                     option also vote for the target venue after
>>                     revisions so that we will not have to delay further.
>>
>>
>>                 I will ask that contributors pick one journal
>>                 from that list - I ask that you REPLY ALL so votes
>>                 will be transparent and time of vote will be
>>                 registered since first to vote will break ties.
>>
>>                 The voting period will be until Tuesday 11-May 1am CDT
>>
>>                 Again, if a journal costs for open publication,
>>                 whoever voted, will split publication costs. If
>>                 anyone on this list is funded for this, please vote.
>>
>>                 I urge contributors to vote - just so that we will
>>                 have a preference order to follow in case of rejection.
>>
>>                 Looking forward to your votes.
>>
>>                             Jacob
>>
>>         _______________________________________________
>>         Vp-reproduce-subgroup mailing list
>>         Vp-reproduce-subgroup at lists.simtk.org
>>         <mailto:Vp-reproduce-subgroup at lists.simtk.org>
>>         https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>>         <https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup>
>>
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