[Vp-integration-subgroup] White paper submitted
Jacob Barhak
jacob.barhak at gmail.com
Thu Apr 29 15:08:12 PDT 2021
Greetings white paper contributors,
After asking Cureus editor for a comprehensive review, the following text
was returned:
"
sure, these are my main concerns:
- Abstract: Non-informative. I read it and the only thing that I learn
is that there is a working group and that they had a discussion that
exposes a reproducibility crisis on modeling. I knew that there was a
reproducibility crisis in all of medicine in general (and modeling in
particular) before. The last sentence claims what the full manuscript is
trying to do. Summarizing the methodology and key findings of the
manuscript in more detail would help the reader decide if this is something
worth reading. Since the abstract is only 64 words long, there is still
plenty of space to do so.
- References: There are plenty of references but several key claims that
I would require a reference for are not supported with evidence. E.g. in
the first paragraph: "*Because of the vast amount of knowledge that has
been gained through epidemic modelling over approximately the past 100
years, it was possible for researchers to quickly adapt their models to
make predictions about the spread and control of the SARS-CoV-2
coronavirus.*“ Were these predictions really that accurate? Has someone
looked at this?
- Self-citation: I understand that we sometimes cite our own papers when
we summarize a space that we are active in. However citing yourself 7 times
as the corresponding author is doing (including citing a video of a
conference talk) makes me wonder if the authors have really searched the
literature for the strongest level of evidence there is.
- Structure: I think this sentence from the manuscript indicates the
main problem of the manuscript: *"**However, upon formation it became
evident that there were many topics of interest, so the large group split
into smaller subgroups that tackle specific topics. This paper is a product
of unifying the work of two sub groups“* The authors propose that
ensuring reproducibility, credibility and utility will lead to easier
integration, which seems correct and would make a nice paper if those
aspects were discussed in that order. This works well until the „Utility of
Models“ section. Suddenly the first sub-heading is „Evaluating model
credibility“ - why wasn’t this discussed in the „Credibility of Models
section“? Towards the end of the paper, based on figure 1, I would expect a
section called „Integration“ that explains the findings of the Model
Integration Subgroup and discusses aspects like ensemble modeling etc.
Instead, there is the "Open Discussion Issues“ section which in itself
isn’t bad but there is nothing that pulls the paper together. The
conclusion remains to general to do that, similar to the abstract.
- Wording: I understand that several people were involved in writing
this but one of the authors should ensure that the manuscript is
comprehensible and has a logic flow. This paragraph for example: "*However,
FDA and Pharmaceuticals are making progress in their drug development pilot
program [26]**. Whatever they come up with to make creditable use of
bio-science models towards design and towards in-silico contributions to
trials. When they formalize their decisions, developers will want to use
model data from relevant MSM tools to reduce trial cost. This opens
opportunities. However, If academic models don’t meet the FDA requirements
to determine credibility of model data, they will not be useful. Industry
is very focused on the regulations and will out-compete academics.
Therefore, it is important that academic practices improve with regards to
repeatability, reproducibility, and reuse. This will create the path
towards credibility and reuse.*“
- What is the progress? That they allow submissions?
- "*Whatever they come up with to make creditable use of
bio-science models towards design and towards in-silico contributions to
trials.*“ I don’t understand that sentence.
- Academic practices have to improve with regards to reuse to create
a path towards reuse?
Maybe split the manuscript in dedicated manuscripts for key topics? This
would allow you to write the manuscript in smaller steps. Right now it
seems like you’re brushing over a lot of aspects that the contributors came
up with even though many are not crucial to the goal of the manuscript.
Normally, I am not that critical if a paper is confusing. But this paper
itself is not reproducible science. It is a narrative/traditional review
with the sole purpose of educating the reader (on an important topic) and
proposing solutions that can then undergo further research. Therefore, as
long as the paper is hard to follow and unpleasant to read, there is no
point in publishing it.
"
This provides us sufficient information to move forward.
Also, I talked to James Glazier via zoom and he told me he will not be
interested in handling this paper forward towards iScience in a short time
period - I interpret this as him withdrawing his vote for a Journal. He
also expressed interest that I continue handling the submission process.
Therefore now we have proper information to proceed and decide where to
submit the paper.
I will send a separate email to reinitiate the voting procedure over the
weekend. Since it will also include resubmission to CureUs after
corrections and option to reopen the paper for modification for a limited
time period. However, I figured it is important that we all get the
information on the editors decision.
I personally disliked the comment about self citation - in a paper composed
by many authors like we did - there will be a lot of self citation - that
is the nature of things - we collect the opinions of many authors. I
don't believe this should be grounds for rejection. Also, it seems that the
rejection is based on style rather than facts, therefore I am not sure if
anything can be corrected to appease such an editor.
If anyone has ideas before I release another vote round, those are welcome.
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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