[Vp-reproduce-subgroup] White paper Revisions

[John Gennari]

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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