[Vp-reproduce-subgroup] White paper submitted
Jacob Barhak
jacob.barhak at gmail.com
Mon Apr 26 05:05:15 PDT 2021
Hi James,
This email is directed to you since you were the one suggesting and voting
for iScience.
Since you suggested iScience and it is an Elsevier Journal, I will ask that
you or someone else handles the submission there - I personally will
not submit to an Elsevier Journal and I just noticed that this is the
publisher when looking for submission information.
I did not notice this when I reduced the options, so since this was my
mistake, I will gladly remove my name so that the group can continue
without me towards this venue.
Alternatively if no one else will handle the submission process in a
reasonable time period of a few weeks, I suggest we vote again on an
alternative venue so I can proceed and handle the submission for the group.
Ideas and comments are welcome from all contributors.
Jacob
On Mon, Apr 26, 2021 at 3:27 AM Jacob Barhak <jacob.barhak at gmail.com> wrote:
> Greetings white paper contributors,
>
> Cureus returned an answer regarding the white paper - they declined the
> submission - in short the rejection is based on style and journal scope.
>
> Since I used the tools provided by the Journal to do the formatting,
> especially of the references - I am confused - I will write the editor, yet
> I suggest we move on to the next voted selection of iScience.
>
> I will start the process quickly and hopefully we will have a better
> response this time.
>
> Jacob
>
>
> #### CureUS response ####
>
>
> Dear authors,
>
> Thank you for your submission. Unfortunately, we must decline this article
> because its practical utility to the medical community is unclear. The
> overall impression one gets from the article is that it has been written
> more in the style of a colloquial summary of a panel discussion than a
> review. This impression is further confirmed by the fact that the article
> refers to itself twice as a white paper. In addition, little attempt has
> been made to adhere to the Cureus author guide (
> https://www.cureus.com/author_guide). Specifically, author affiliations
> contain acronyms, the subheadings are not in the sentence case, spaces and
> bulleted lists have been used haphazardly throughout the article, and
> reference formatting is almost nonexistent.
>
> We would encourage you to submit your next article to Cureus provided it
> falls within the scope of the journal. Thanks for your time.
>
> On Thu, Apr 22, 2021 at 4:50 AM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
>
>> Greetings White paper contributors,
>>
>> Since no objection was raised the paper was just submitted to Cureus as
>> previously elected.
>>
>> You will find an updated version after changes necessary for submission
>> were implemented in this link:
>>
>> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>>
>>
>> The changes were mostly minor typos and reference management - a few
>> references needed correction and one was deleted since it no longer showed
>> any relevant information.
>>
>> to give you all perspective - only formatting and handling of references
>> towards publication in the necessary format took 2 work days dedicated for
>> this alone.
>>
>> So all those who want to add anything to the paper to be considered post
>> review, I urge you to:
>> 1. submit any changes now - do not wait - once the review is returned no
>> changes or additions will be considered and my experience is that Cureus
>> provides review rapidly, so time is limited.
>> 2. If you add references, please provide a DOI / link to help process
>> those. And please avoid adding many references - processing those takes a
>> long time.
>> 3. Do not send changes to me alone using reply - please use REPLY ALL so
>> everyone will see the discussion - we want to be as transparent as possible
>>
>>
>> I hope for a quick review process.
>>
>> Jacob
>>
>>
>> On Fri, Apr 16, 2021 at 6:08 PM Jacob Barhak <jacob.barhak at gmail.com>
>> wrote:
>>
>>> 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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