[Vp-integration-subgroup] [Vp-reproduce-subgroup] White paper submission - vote for venue
Jacob Barhak
jacob.barhak at gmail.com
Sun May 2 08:42:48 PDT 2021
Hi Gilberto,
Your message must get some response from me.
The self citations the editor wrote about are mine - yet many contributors
have self cited - and self citation is not really an issue. It expresses
the opinion of the persons signed on the paper. I did not see any
objections to those references and please note that my references are
partially to patented technology - so if anyone else does similar work in
the US - they better communicate with me beforehand. And please note that I
did declare conflict of interest multiple times including in the paper -
and once declared publicly this should not be an issue. In fact there are
multiple leads for these subgroups partially at my request to allow proper
function in case of a conflict of interest.
Therefore unless you know how to rewrite the paper without my references,
or convince me to remove those there is no simple way we can address this
editor's comments to his satisfaction.
Specifically the video the editor pinpointed is:
-
Jacob. Barhak, Open Source and Sustainability, COMBINE 2020 October 5-9.
Video: *https://drive.google.com/drive/folders/1actGnx6FwvoCcPrrF3qbnO0AmHt10WN6
<https://drive.google.com/drive/folders/1actGnx6FwvoCcPrrF3qbnO0AmHt10WN6>*
starting from minute 13:10. Presentation:
*https://jacob-barhak.github.io/COMBINE2020_OpenSource_upload_2020_10_04.odp
<https://jacob-barhak.github.io/COMBINE2020_OpenSource_upload_2020_10_04.odp>*
If please check out my arguments in this talk and decide for yourself if
this is not worth as a citable reference. If you want to open the
discussion on licenses, I can add that I personally have been negatively
affected due to licensing issues and my conclusion is that CC0 is a good
solution to share code and data to some cases and there is an increasing
number of entities realizing it - at least one cited in the paper. We can
explore this issue deeper, yet I think the version in the paper is good
enough and the editor rejected the paper due to style issues and not due to
substance and accuracy issues - I think the editor made a bad decision and
in fact my communication with the editor in chief did change the response,
meaning that there was an issue on the side of the Journal - not our group.
This is my personal opinion, yet it is more important for the group to
decide here since we are many people that need to reach unanimous consensus.
Note, however, that I do ask that whoever wants to introduce the changes
will do the hard work of making sure that:
1. They make the edits - I did enough - if you want a change you need to do
the leg work.
2. They comply with the target journal format - this means also making sure
references are properly ordered and cited and do this properly coordinated
amongst all the changes flowing in.
3. Unanimous consensus is established before submission - this is actually
a legal requirement - without that we cannot submit to a 3rd party that
will ask for copyright transfer.
4. We do this in a timely manner and finish in about 4 weeks from now.
So all those who voted, will actually have to act to make your vote
materialize. The sooner you start, the better.
I hope my response is clear enough to understand some of the difficulties
and that we can clear those.
Jacob
On Sun, May 2, 2021 at 9:47 AM Gilberto Gonzalez-Parra <
gilberto.gonzalezparra at nmt.edu> wrote:
> I agree with option 13. We should focus on the comments of the editor of
> Cureus. Very briefly and seen the big picture. These are the main aspects
> that she/he commented:
>
> *Abstract:* Emphasize the reproducibility issue (the editor said he knew
> about it but not everyone knows). Explain methodology (review,
> discussions, seminars, etc), key findings, and proposed ideas to solve the
> reproducibility issues.
>
> *Structure and message*: Take into account the editor's comment *"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."*. I think a diagram
> would help to organize the ideas for us and readers. Maybe the open
> discussion issues section can be renamed just to Discussions and try to put
> the ideas more organized with some particular purpose based on the previous
> sections. In the conclusions, send a more clear message about the purpose
> of the paper. For instance key findings, and proposed ideas to solve the
> reproducibility issues.
>
> *References*: Try to support the claims with at least one or two
> references. Some things in life are subjective (even sometimes seem
> obvious), so giving references from previous authors helps to the
> credibility of the paper. The editor (cureus) raised some issues regarding
> references and video of a conference talk. Usually it is better to support
> the paper with references that have been already peer-reviewed to give a
> more solid base. This is how the paper review process and journal works.
>
>
> Best regards,
>
>
> ***************************************************************************
> Gilberto C. Gonzalez-Parra, Ph.D in Applied Mathematics.
> Faculty of the Mathematics Department
> New Mexico Tech, NM, USA.
>
> ****************************************************************************
>
>
> On Sat, May 1, 2021 at 10:36 PM Winston Garira <
> Winston.Garira at univen.ac.za> wrote:
>
>> I agree with making revisions- 13!
>>
>> WIinston
>>
>> Get Outlook for iOS <https://aka.ms/o0ukef>
>> ------------------------------
>> *From:* Dr. Rahuman Sheriff <sheriff at ebi.ac.uk>
>> *Sent:* Saturday, May 1, 2021 11:42:11 PM
>> *To:* James Glazier <jaglazier at gmail.com>
>> *Cc:* William Waites <wwaites at ieee.org>;
>> vp-reproduce-subgroup at lists.simtk.org <
>> vp-reproduce-subgroup at lists.simtk.org>;
>> vp-integration-subgroup at lists.simtk.org <
>> vp-integration-subgroup at lists.simtk.org>; Jonathan Karr <
>> jonrkarr at gmail.com>; John Gennari <gennari at uw.edu>; Winston Garira <
>> Winston.Garira at univen.ac.za>
>> *Subject:* Re: [Vp-integration-subgroup] [Vp-reproduce-subgroup] White
>> paper submission - vote for venue
>>
>> I agree with 13 - revision.
>> Sheriff
>> Sent from my iPhone
>>
>> On 2 May 2021, at 02:34, James Glazier <jaglazier at gmail.com> wrote:
>>
>>
>> I believe the manuscript must be revised before submission. As presented
>> now it does not do justice to the great ideas provided by the many
>> contributors.
>> I am indifferent to the venue of publication. RS Interface or
>> Bioinformatics are both fine, but I am happy to see it published anywhere
>> (as long as it is cleaned up). Bulletin of Mathematical Biology had
>> Reinhard as chief editor, so you would at least get a review....
>>
>> JAG
>>
>> On Sat, May 1, 2021 at 4:22 PM William Waites <wwaites at ieee.org> wrote:
>>
>> Agree on 13 revision, though I am severely time-constrained for the next
>> few weeks.
>>
>> No strong preference on venue but it’s good to have an idea of the
>> audience we’re writing for. I like RS Interface or Bioinformatics. If this
>> gets done before my MRC funding runs out, they will pay OA fees.
>>
>> Cheers,
>> -w
>>
>>
>> > On 1 May 2021, at 20:38, Eric Forgoston <eric.forgoston at montclair.edu>
>> wrote:
>> >
>> > 13 - open for revision; no preference on venue.
>> > ---------------------
>> > 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/
>> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Feric-forgoston.github.io%2F&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C66fc4261f4fb459414d708d90ce9fee3%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637555021414684464%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6PTWhvVbSOhetbZypl2z4dICfg1WIZ5gvtIwQ1HhKos%3D&reserved=0>
>> >
>> >
>> > On Sat, May 1, 2021 at 1:32 PM Jonathan Karr <jonrkarr at gmail.com>
>> wrote:
>> > #13 -- revise
>> >
>> > On Sat, May 1, 2021 at 1:18 PM Jacob Barhak <jacob.barhak at gmail.com>
>> wrote:
>> > Greetings white paper contributors,
>> >
>> > It is time to vote again for the target venue. Here are the options
>> again.
>> > • Cureus - resubmission after addressing editor comments
>> > • 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
>> > • bulletin of mathematical biology
>> > • Bioinformatics.
>> > • Do not submit now - instead open for revisions for 2 weeks and
>> then submit. If you choose this option also vote for the target venue after
>> revisions so that we will not have to delay further.
>> >
>> > I will ask that contributors pick one journal from that list - I ask
>> that you REPLY ALL so votes will be transparent and time of vote will be
>> registered since first to vote will break ties.
>> >
>> > The voting period will be until Tuesday 11-May 1am CDT
>> >
>> > Again, if a journal costs for open publication, whoever voted, will
>> split publication costs. If anyone on this list is funded for this, please
>> vote.
>> >
>> > I urge contributors to vote - just so that we will have a preference
>> order to follow in case of rejection.
>> >
>> > Looking forward to your votes.
>> >
>> > Jacob
>> > _______________________________________________
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>>
>>
>>
>> --
>> James A. Glazier, PhD
>> Professor of Intelligent Systems Engineering, Adjunct Professor of Physics
>> Director Biocomplexity Institute
>> Indiana University, Bloomington
>> (812) 391-2159
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