[Vp-integration-subgroup] [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
>>
>> _______________________________________________
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>> Vp-reproduce-subgroup at lists.simtk.org
>> <mailto:Vp-reproduce-subgroup at lists.simtk.org>
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>> <https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup>
>>
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