[Vp-integration-subgroup] [Vp-reproduce-subgroup] White paper revision
Jacob Barhak
jacob.barhak at gmail.com
Fri May 14 18:05:46 PDT 2021
Thanks John,
These are first impressions. You kept the important things unchanged - this
is important.
I personally like the title change - it gives a purpose and is much less
dry
I also like that you kept most of the topics intact - for some reason you
removed validation barriers - perhaps it should be indeed added to the end
of the paper in unresolved issues - we can discuss this.
My only concern is that you removed a lot of text contributed by multiple
authors - this will complicate reference adjustments, yet more importantly
it will remove whole ideas generated by people who contributed - we need to
address this somehow - perhaps we can talk about it on Monday.
I am indifferent about removing the process we went through and the working
group - if interesting, perhaps it can be added as an appendix. Yet I will
personally not miss those sections if they disappear. Yet I can see the
mess with the references already - I do not envy the person that needs to
fix it.
We will also need to integrate this with ideas Sheriff had in his version -
he also did some work we should incorporate
Yet this is a good start. Hopefully we can finalize this quickly, approve,
submit and move forward to solve those issues.
Jacob
-
On Fri, May 14, 2021 at 7:34 PM John Gennari <gennari at uw.edu> wrote:
>
> 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> 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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