[Vp-integration-subgroup] White paper Venue Voting results and next steps

Jacob Barhak jacob.barhak at gmail.com
Fri Apr 16 16:08:57 PDT 2021 

Greetings white paper contributors

The voting period on the venue has ended and the selected venue we will
send the white paper to is Cureus.

John Rice and myself voted for that venue and will cover the publication
fees.

In case of any issue with this venue we will move to iScience that James
Gazier voted for.

The paper will need formatting to fit the venue - it handles references in
a specific way. However, I intend to mostly cut and paste the text in this
version - without change:
https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing

The process we went through ensures we reach a level of consensus and that
the manuscript can be legally submitted on behalf of you all. If anyone has
any strong objections to stop the submission process, please stop now.
Otherwise I will start the submission process next week.

Please remember this is a large team with many people so there will be
compromises. Moreover, the paper will undergo review and we will have to
make changes.

During the writing process I presented some deadlines and denied
contributions that happened after the deadline was over. I know Tomas
Halikar wanted to contribute and now Jim Saluka wants to contribute. I also
know John Gennari schedule prevented him from properly reviewing the paper
and I know that Sheriff asked for several modifications. All this can be
corrected when the paper gets reviewed and we get the review - we will then
open the paper for modifications and potentially other contributions.
However, the time then will be limited, so to conserve time, I suggest that
those interested in changes or additions, continue the discussion in
parallel to the formal submission process.

Cureus review process is typically quick compared to many venues I
encountered in the past. Once the paper comes back from review we will have
limited time to respond, so to conserve time I will consider only text that
we submitted and contributions.modifications made until that time. So if
you have any important additions, please create your own copy of the
document and publicly share the link with these mailing lists. Similar to
what Sheriff did.

So please do not stop discussion on the paper - As Jonathan Karr suggested,
we may have different versions suitable for different venues so your
contributions are valuable - however, for the sake of getting our work
published I ask that we do things in a timely manner.

Again, if you have things to communicate about the paper - do not wait
until review is back - it will be too late then - instead comment now so
your contributions can be considered when post review modifications start.

I hope we have a fast review and can make this work amplified by Cureus
soon.

            Jacob



On Thu, Apr 15, 2021 at 7:13 PM Jacob Barhak <jacob.barhak at gmail.com> wrote:

> Greetings Contributors,
>
> Since there are only a few hours before the voting period ends, I will
> vote to break a tie between CureuUs and iScience.
>
> I was about to abstain, yet it seems the tie needs to be broken
> distinctively.
>
> I will vote for Cureus. My reasons are:
> - I am familiar with this venue submission process
> - the venue has opened up to allow more references - thus dismissing my
> original remark on it
> - I will be the person handling submission and it will save me time to
> submit somewhere familiar.
> - The review process in this venue is relatively fast.
> - It has an option for rushed pubmed central publication
> - the open publication costs are reasonable compared to many other venues
>
> Unless 3 other people will vote for another venue in the next few hours,
> it seems this is the venue that the paper will be submitted to for review.
> However, things may change.
>
> John and I will split the publication costs since we both voted on this
> venue.  If anyone else wants to split costs, feel free to publicly vote for
> this venue - otherwise it will be John and myself.
>
> Please note that there are a few more hours to vote - a bit less than 6
> hours from the time of this email - if you support another conclusion for a
> venue, you are welcome to vote.
>
>                  Jacob
>
>
>
>
> On Wed, Apr 14, 2021 at 11:03 AM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
>
>> Greetings white paper contributors,
>>
>> Please vote on a venue for the paper. There are less than two days to
>> vote to influence the submission venue.
>>
>> We had 2 votes by now
>> Cureus by John Rice
>> iScience by James Glazier
>>
>> John Rice was first,  yet did not reply to all as requested and sent me
>> the email - I forwarded his vote to the list first. James was the first
>> that replied to all,  so technically he is the first valid vote.
>>
>> So currently there is a tie that should be broken by first vote which is
>> open to interpretation. Since time is running out,  I suggest people choose
>> to make the choice distinctive, otherwise I will vote to break the tie and
>> was hoping to avoid voting since I had a lot of influence already and
>> wanted to yield control.
>>
>> So please,  if you have a preference on venue,  please vote for one venue
>> by 1am CDT  April 16th.
>>
>>
>> I hope we have a conclusive decision.
>>
>>          Jacob
>>
>>
>>
>>
>> On Mon, Apr 12, 2021, 17:17 James Glazier <jaglazier at gmail.com> wrote:
>>
>>> iScience
>>> James A. Glazier
>>>
>>> On Mon, Apr 12, 2021 at 12:40 PM Jacob Barhak <jacob.barhak at gmail.com>
>>> wrote:
>>>
>>>> Greetings White paper Contributors,
>>>>
>>>> This is your chance to decide on the venue. If you name is on this
>>>> list, please take a few minutes anv vote for the venue:
>>>> Jonathan Karr
>>>> Rahuman Sheriff
>>>> James Osborne
>>>> Gilberto Gonzalez Parra
>>>> Eric Forgoston
>>>> Ruth Bowness
>>>> Yaling Liu
>>>> Robin Thompson
>>>> Winston Garira
>>>> Marcella Torres
>>>> Hana M. Dobrovolny
>>>> Tingting Tang
>>>> William Waites
>>>> James Glazier
>>>> James R. Faeder
>>>>
>>>> Currently one vote was cast and unless there will be more votes, the
>>>> venue voted for will be chosen. So if you have a strong preference, this is
>>>> your chance to influence the publication venue.
>>>>
>>>> You will find eligible venues below as well as additional details.
>>>>
>>>> I look forward to your votes.
>>>>
>>>>                Jacob
>>>>
>>>>
>>>>
>>>> On Thu, Apr 8, 2021 at 7:04 PM John Rice <john.rice at noboxes.org> wrote:
>>>>
>>>>> No objection to any but will VOTE CUREUS.
>>>>>
>>>>> My understanding it was created to provide a peer reviewed open source
>>>>> indexed journal that could accommodate new forms of papers and new relevant
>>>>> topical areas.  Good timing for them lifting the limit on references, so
>>>>> assume this paper could be submitted in current form subject only to
>>>>> reviewers’ response.
>>>>>
>>>>> Don’t know that it has a model credibility related topic section yet.
>>>>>
>>>>> John
>>>>>
>>>>>
>>>>>
>>>>> Typed with two thumbs on my iPhone.  (757) 318-0671
>>>>>
>>>>> “Upon this gifted age, in its dark hour,
>>>>> Rains from the sky a meteoric shower
>>>>> Of facts . . . they lie unquestioned, uncombined.
>>>>> Wisdom enough to leech us of our ill
>>>>> Is daily spun; but there exists no loom
>>>>> To weave it into fabric.”
>>>>>
>>>>> –Edna St. Vincent Millay,
>>>>>
>>>>>
>>>>>
>>>>> On Apr 8, 2021, at 01:23, Jacob Barhak <jacob.barhak at gmail.com> wrote:
>>>>>
>>>>> 
>>>>> Greeting White paper contributors,
>>>>>
>>>>> The old Thread that contained discussions towards creations and
>>>>> approval of the white paper have become too long, so I started a new maling
>>>>> thread.
>>>>>
>>>>> You can find the old discussion thread here:
>>>>>
>>>>> https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-April/000052.html
>>>>>
>>>>> To summarize, we have reached a point where 17 authors approved the
>>>>> following version for submission, pending some minor changes like
>>>>> spelling and grammar correction.
>>>>>
>>>>> To avoid any confusion - here is the paper version we approved is here:
>>>>>
>>>>> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>>>>>
>>>>> At this point we need to select a venue to submit the paper to. Here
>>>>> is a short list I collected after incorporating all the suggestions and
>>>>> removed all venues that had any objections. To your convenience I added
>>>>> additional notes form personal knowledge - I did not look at issues such as
>>>>> publication fees for open access - different venues may have different
>>>>> rules and may require some additional investment, so please look at the
>>>>> venue you are choosing and learn the limitations/benefits before you vote:
>>>>>
>>>>> Here is the short list:
>>>>>
>>>>>    1. Cureus - will require cutting out some references due to
>>>>>    limitation
>>>>>    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. iScience
>>>>>    12. bulletin of mathematical biology
>>>>>    13. Bioinformatics.
>>>>>
>>>>>
>>>>> I ask that each contributor who has a preference among those Journals
>>>>> reply to all to this message and pick one venue. Please pick only one
>>>>> considering all aspects of the venue. You are welcome to include your
>>>>> reasoning, yet vote towards only one venue.  You are welcome to change your
>>>>> mind - yet only your last vote will count.
>>>>>
>>>>> In case of a tie in the number of votes, the venue that got the first
>>>>> counted vote will be chosen.
>>>>>
>>>>> After we select, I will put the work to format the submission towards
>>>>> that venue and include all necessary submission matters. In case of fees,
>>>>> those who voted for the venue will be responsible for covering publication
>>>>> fees.
>>>>>
>>>>> At this point I assume no one has any objections to any venues and we
>>>>> are all ok with submitting this version - so we are just prioritizing
>>>>> according to the majority of wishes while keeping the process transparent
>>>>> and giving some incentive to early bird vote.
>>>>>
>>>>> If any of my assumptions are not correct, please correct me now!
>>>>>
>>>>> This is the best way I think we can create consensus in such a large
>>>>> group - and consensus is legally necessary for publication.
>>>>>
>>>>> I ask that we limit the voting time to approximately one week. So
>>>>> votes should be cast by 1am April 16th CDT.
>>>>>
>>>>> I will send another reminder during this week, yet I assume one week
>>>>> is sufficient to make a simple choice of prefered venue and those not
>>>>> voting elect to abstain from choosing and prefer the majority choice.
>>>>>
>>>>> I look 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
>>>>>
>>>> _______________________________________________
>>>> Vp-reproduce-subgroup mailing list
>>>> Vp-reproduce-subgroup at lists.simtk.org
>>>> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>>>>
>>>
>>>
>>> --
>>> James A. Glazier
>>> Indiana University
>>>
>>
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