[Vp-integration-subgroup] [Vp-reproduce-subgroup] White paper revision
John Gennari
gennari at uw.edu
Fri May 14 17:34:18 PDT 2021
Easy-peasy. Attached, find a marked up "differences" version. As you
might guess, it's almost completely "red ink". Fee
-John G.
On 5/14/2021 4:43 PM, Jacob Barhak wrote:
> Hi John,
>
> You removed massive parts - can you share the changes made from the
> original - there is a reason I opened up the paper for changes - we
> need to see what was changed - Can you please somehow send a
> differential version with changes highlighted?
>
> Hopefully this is attainable.
>
> Jacob
>
> On Fri, May 14, 2021 at 4:48 PM John Gennari <gennari at uw.edu
> <mailto:gennari at uw.edu>> wrote:
>
>
> 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
> <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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