[Vp-reproduce-subgroup] White paper Revisions

[Jacob Barhak]

Hi John,

You are more than welcome to rejoin the effort and introduce editing.
However, Voting will continue since people can change their votes and
change venues until the deadline. People who voted have to understand the
implications of their vote - they themselves need to act - no one will do
it for them.

Yet I agree it is good to have a discussion. In fact, this is what we were
doing for a while when this paper was initially formed - look at the many
versions and the comments by many people on the original documents - this
was our discussion.

We will not know the venue to format to after the deadline, yet until then
we are welcome to suggest ideas. The only thing I ask is to be efficient
and not waste time - there is a reason I imposed deadlines - this can go on
forever. Remember that our fall back is the last consensus point if we do
not reach unanimous consensus within approximately 4 weeks. In other words,
unless we act, we waste 4 weeks.

Discussion is welcome , yet I suggest avoiding style related topics such as
"belong in a peer reviewed scientific piece" - style is subjective and in
the eyes of the beholder. Notice that in the paper we actually criticize
the peer reviewed scientific Journals that publish non-reproducible science
and Sheriff can tell you how many corresponding authors return an answer to
queries to papers they published in scientific literature - so let us
please focus on what is important and do it in a timely manner. In 4 weeks
it will be about half a year after we started - if we cannot reach
consensus in that time period, it implies something about us as a group.
Hopefully we all understand this.

So I suggest starting to act. The sooner the better.

              Jacob

On Mon, May 3, 2021 at 4:25 PM John Gennari <gennari at uw.edu> wrote:

> Greetings, all:
>
> Although it is still a long ways until the voting deadline (see email
> below from Jacob), I see enough votes for "Revise the manuscript" (#13)
> that I felt encouraged to look again at the manuscript, and review it with
> an eye toward revisions. As I stated back in March, the general topic of
> manuscript is good, and one that I would be very willing to help with, but
> at the time, the deadlines were too short for me to be included as a
> co-author. Jacob was explicit about welcoming me to join back in when the
> paper is ready to be revised, and I am taking this vote (and his email
> encouraging us to "start preparing revisions") to mean that's occurring
> now.
>
> I have carefully read thru the draft manuscript, and I have many ideas for
> improvement. However, it is challenging to provide constructive criticism
> to such a large group effort, especially when I do not even know the
> majority of people involved. I don't want to be overly critical--my goal is
> to provide constructive ideas for improvement. But all of us have different
> perspectives about what is and isn't important. It's really an open
> question whether there is enough consensus among us all to write a single,
> coherent paper.
>
> Those caveats aside, here are the main bullet points of my "thoughts for
> improvement".
>
> *1* The paper needs improved organization. The current introduction does
> not make clear what the main messages and goals of the manuscript are.
> Although not as explicit as I would like, I think the paper does have some
> good messages -- indeed, these are captured nicely in Figure 1 and Table 1.
> In my view, the current version of the introduction should be shortened
> dramatically, allowing the reader to quickly get to Figure 1 and Table 1.
> In fact, Table 1 provides a nice organization to the meat of the paper: 13
> rows representing 13 problems, which are discussed in 13 subsequent
> sections. If this organization were made explicit, it would provide a lot
> more clarity, and make things much easier for readers (and reviewers!).
>
> *2* As has been noted by others on this list, the 13 sections are clearly
> written by different authors, and thus appear disjointed. One way to
> ameliorate this problem would be to have a discussion section that connects
> these 13 sections, describing synergies among the 13 rows of Table 1. In
> the current manuscript, the discussion section does not include any
> additional information or organization of the 13 rows, but instead is a
> rough set of notes about "things that were mentioned but not discussed".
>
> *3* In my opinion, usually organizational issues, such as working groups,
> and subgroups thereof, do not really belong in a peer reviewed scientific
> piece. Of course, these organizations need to be properly acknowledged. But
> why would the general scientific public care that this paper arose from two
> (and not 3 or 4) subgroups of people? Better to move directly to the
> science without talking about working groups. For example, it might be an
> excellent idea to talk about the link between modeling of multi-cell
> physiology (in one individual) and the modeling of viral spread in a
> population of individuals.
>
> *4* I remain confused about the role of population-based modeling in this
> manuscript. One of the working groups is titled "viral pandemics", but
> there is very little here that is specific to population-based models. In a
> few places (e.g., the section on stochastic modeling) there are examples
> drawn from that domain, but otherwise, the 13 rows are about challenges in
> modeling generally, and not specific to population-based modeling. The
> opening paragraph talks about the SIR models and about COVID-19, but the
> rest of the manuscript doesn't follow through. The paper would be stronger
> in either direction: (a) Either talk more about population based modeling
> and pandemics or (b) changing the opening paragraph to better fit the
> broader focus of modeling physiology and pathology in general.
>
> Those are my main points. I would imagine that they could initiate debate
> and disagreement and I'm certainly not going to try to impose my vision on
> all of you. I would guess that points 3 and 4 might be the most
> controversial; unfortunately, these must be settled in some manner before
> we can write a good introduction to the paper.  But if there are points in
> the above that all agree on, then I could quickly (within a week) make an
> editing pass over the manuscript to implement some of the above ideas.
>
> I also have more detailed notes about specific section and rows of the
> table, but I will save those for later, after I hear back about the above.
>
> Sincerely,
>
> John Gennari
>
>
> On 5/1/2021 10:18 AM, Jacob Barhak wrote:
>
> Greetings white paper contributors,
>
> It is time to vote again for the target venue. Here are the options again.
>
>    1. Cureus - resubmission after addressing editor comments
>    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. bulletin of mathematical biology
>    12. Bioinformatics.
>    13. 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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