[Vp-reproduce-subgroup] White paper revision
Jacob Barhak
jacob.barhak at gmail.com
Fri May 14 16:43:52 PDT 2021
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> 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
> (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/
>
>
> On Wed, May 12, 2021 at 2:09 PM John Gennari <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/
>>
>>
>> On Tue, May 11, 2021 at 10:26 AM Jacob Barhak <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
>>>
>>> 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
>>>
>>> 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>
>>> 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>
>>>> 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
>>> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>>>
>>
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