<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<p>Greetings, all: <br>
</p>
<p>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. <br>
</p>
<p>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.</p>
<p>Those caveats aside, here are the main bullet points of my
"thoughts for improvement". <br>
</p>
<p>*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!). <br>
</p>
<p>*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". <br>
</p>
<p>*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. <br>
</p>
<p>*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. <br>
</p>
<p>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.</p>
<p>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.<br>
</p>
<p>Sincerely, <br>
</p>
<p>John Gennari</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 5/1/2021 10:18 AM, Jacob Barhak
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAM_y+3R10QVCHQFSPkbh3MYCS9Xuqnk-q0v8_u5SdrzFxtdoDQ@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Greetings white paper contributors,
<div><br>
</div>
<div>It is time to vote again for the target venue. Here are the
options again. </div>
<div>
<div>
<ol>
<li style="margin-left:15px">Cureus - resubmission after
addressing editor comments</li>
<li style="margin-left:15px">Nature - if you <span
class="gmail-il">vote</span> for this venue please
specify flavour such as Nature Scientific Reports</li>
<li style="margin-left:15px">Science</li>
<li style="margin-left:15px">Briefings in Bioinformatics</li>
<li style="margin-left:15px">Trends in Biotechnology -
requires distilling the paper</li>
<li style="margin-left:15px">Journal of The Royal Society
Interface<br>
</li>
<li style="margin-left:15px">Annual Review of Public
Health<br>
</li>
<li style="margin-left:15px">BMJ</li>
<li style="margin-left:15px">Annual Review of Biomedical
Engineering<br>
</li>
<li style="margin-left:15px">F1000research - if you <span
class="gmail-il">vote</span> for this this venue
please specify Gateway / Collection </li>
<li style="margin-left:15px">bulletin of mathematical
biology<br>
</li>
<li style="margin-left:15px">Bioinformatics.<br>
</li>
<li style="margin-left:15px">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. </li>
</ol>
<div><br>
</div>
</div>
<div>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.</div>
<div><br>
</div>
<div>The voting period will be until Tuesday 11-May 1am CDT </div>
</div>
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>I urge contributors to vote - just so that we will have a
preference order to follow in case of rejection.</div>
<div><br>
</div>
<div>Looking forward to your votes. </div>
<div><br>
</div>
<div> Jacob</div>
</div>
</blockquote>
</body>
</html>