[Vp-integration-subgroup] [Vp-reproduce-subgroup] White paper submission - vote for venue

Sun May 2 07:47:10 PDT 2021

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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