[Vp-integration-subgroup] [Vp-reproduce-subgroup] White paper submitted
Jacob Barhak
jacob.barhak at gmail.com
Tue Apr 27 11:31:01 PDT 2021
Thanks William,
If you value my efforts, please make sure this gets distributed as soon as
possible. It is more important than my name appearing in some place - John
Genarri also understood this and chose to speed up matters and remove his
name- I am ok to do the same if this speeds up the process.
Whatever way moves this faster is ok with me.
Jacob
On Tue, Apr 27, 2021 at 1:23 PM William Waites <wwaites at ieee.org> wrote:
> For what it’s worth, I do not want you to remove your name, Jacob. You
> have put a lot of time and energy into this and pushed it forward. It would
> not be fair to remove you.
>
> How about Royal Society Interface?
>
>
> > On 27 Apr 2021, at 18:58, Jacob Barhak <jacob.barhak at gmail.com> wrote:
> >
> > Thanks Sheriff, Thanks Jonathan, Thanks Eric,
> >
> > Your suggestions are much appreciated, yet if you do not mind, I will
> follow a protocol that ensures we are in consensus. James wrote to me
> privately after I suggested he pursue his selection. My understanding is
> that he wants a revision - it seems you all want revisions before
> submission.
> >
> > However, I do not want revisions at this point since this will force
> re-establishing consensus. This process is time consuming and many of you
> do not see the efforts behind the scenes of making it happen.
> >
> > Sheriff, I do not view Cureus recommendations as binding or even helpful
> - it is clear something wrong happened at the editorial board there - I
> wrote to the editor and he is checking what happened. However, I suggest we
> move on to another venue and speed up the process. You see, my
> consideration is releasing the paper for 3rd party publication as soon as
> possible. Any delays in the name of perfection actually diminish any
> potential impact we may have. The amount of knowledge we assembled should
> be amplified by quick redistribution - not constant modification that never
> ends in the name of perfection.
> >
> > We will have the opportunity for adding more knowledge after we get
> proper review - Cureus laconic response you see is not proper review! I was
> disappointed to see this since the Journal did show promise in the past.
> >
> > My suggestion to remove my name was to speed up the publication process
> - it is more important to release this paper than to have my name there.
> Think about it, the amount of knowledge we accumulated and the level of
> consensus we established are actually a call for action that can have great
> impact and with proper exposure may drive policy - so the sooner this is
> distributed, the better. My personal preferences should not be in the way.
> >
> > The current decision point is by James - if he takes over the submission
> to iScience and does this quickly - we have consensus. Paper goes to review
> without my name and its ok.
> >
> > If he chooses to withdraw his suggestion - we need to decide again on a
> target venue and vote - which will take about a week to allow everyone to
> respond.
> >
> > Hopefully James will decide quickly so we can restart the process
> quickly.
> >
> > Jacob
> >
> >
> > On Tue, Apr 27, 2021 at 11:53 AM Dr. Rahuman Sheriff <sheriff at ebi.ac.uk>
> wrote:
> > I agree. Let’s select a venue that is not in the exclusion list.
> > Those who didn’t see the feedback from the Cureus, Please find it below.
> > Sheriff
> >
> > 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 27 Apr 2021, at 21:43, Jonathan Karr <jonrkarr at gmail.com> wrote:
> >>
> >>
> >> I second those suggestions -- pick a venue that Jakob supports and make
> edits to address the Cureus editor's feedback. I'd also like to see the few
> additional people that wanted to contribute invited.
> >>
> >> Jonathan
> >>
> >> On Tue, Apr 27, 2021 at 11:59 AM Eric Forgoston <
> eric.forgoston at montclair.edu> wrote:
> >> Dear all,
> >>
> >> I suggest we find an alternate venue so that Jacob does not need to
> remove his name. Since that will take a bit of time, it may be worthwhile
> to simultaneously have those individuals who wanted to make content changes
> do so. This is likely beneficial given that Cureus already has noted some
> issues, but I leave it to Jacob to decide.
> >>
> >> Best wishes,
> >>
> >> 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 Mon, Apr 26, 2021 at 8:05 AM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
> >> 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:
> >> • Cureus - will require cutting out some references due to
> limitation
> >> • Nature - if you vote for this venue please specify flavour such
> as Nature Scientific Reports
> >> • Science
> >> • Briefings in Bioinformatics
> >> • Trends in Biotechnology - requires distilling the paper
> >> • Journal of The Royal Society Interface
> >> • Annual Review of Public Health
> >> • BMJ
> >> • Annual Review of Biomedical Engineering
> >> • F1000research - if you vote for this this venue please specify
> Gateway / Collection
> >> • iScience
> >> • bulletin of mathematical biology
> >> • 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
> >> _______________________________________________
> >> Vp-integration-subgroup mailing list
> >> Vp-integration-subgroup at lists.simtk.org
> >> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
> >> _______________________________________________
> >> Vp-integration-subgroup mailing list
> >> Vp-integration-subgroup at lists.simtk.org
> >> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
> > _______________________________________________
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> > Vp-integration-subgroup at lists.simtk.org
> > https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
> > _______________________________________________
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> > https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>
>
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