[Vp-integration-subgroup] [Vp-reproduce-subgroup] White paper submitted
William Waites
wwaites at ieee.org
Tue Apr 27 11:23:03 PDT 2021
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
>>
>>
>>
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>>
>> --
>> James A. Glazier
>> Indiana University
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