<div dir="ltr">Thanks John,<div><br></div><div>The fixes you ask seem mostly minor to me and some were anticipated and marked. We have not yet decided on a target venue and there will be more minor changes after paper review and another round of approvals that will follow. </div><div><br></div><div>For now I am trying to make things manageable by getting people to agree to submit - I do not know about you, yet I only once saw a paper that got accepted without changes requested by reviewers, and I must add it was not a major breakthrough - so I blame review. My request to approve the paper is necessary from a legal perspective - Otherwise I am not allowed to submit in your names. I frankly do not trust academics to be practical and I believe you sensed it. And I am trying to complete a task the working group leads, that are also academics, tasked us. This means we need to get to a level where all those who contributed are ok with paper submission - this means they agree with the text and what others wrote and I edited.</div><div><br></div><div>The agreement should be at the level of good enough for submission - not final product. </div><div><br></div><div>You ask to delay the paper until after a conference. This seems too much to get approvals - we waited long enough anyway . How about this compromise?</div><div><br></div><div>1. I fixed the text issue in pages 14-15 you mentioned - those are minor - check the version history for recent changes. </div><div><br></div><div>2. I would love SemGen to be mentioned. Notice that Reference [G2] that you provided before was not referenced in the text you provided- I actually commented on it for your correction - look at the comments - some of those require your approval - you have to provide information on where to mention it. And when we say tool - we also include the SBML language - a language is a communication tool after all - so it does not change anything. Yet if you think SemGen is approprite to be listed in the table near SBML-comp - please tell me how to do it. I know little about those and need the expert to instruct me where to make the change. You are this expert - please help yet please keep the change minor. </div><div><br></div><div>3. You want to add another reference. Let us please wait until the review is done for more modifications - otherwise this will never end - every author will want to add more references and if you allow one, this will never finish. However, after review, we will open up the paper for more changes in which you can add the last reference you sent me by email. </div><div><br></div><div>4. The open issues section at the end is important since it includes issues we will address in the future and people felt that some of the topics there are important. We will cut the paper according to venue requests after review - I know there are repeated ideas, yet I decided not to remove ideas anyone contributed - this would be a kind of censorship and I only trimmed the paper in some places that were absolutely necessary. After Review we can reopen the issues since there will be another round of approvals. </div><div><br></div><div>5. ModelXchange is already mentioned in the paper - Jonathan Karr added it so unless you have objections to it being added there is no need to wait for a conference.</div><div><br></div><div>6. If you want to iterate through the text and find typos and grammar issues, that is fine. Hana Dobrovolny did this in the past and many approved already, so I assumed it was good enough , yet if you are more particular, please go ahead. However, if you intend to make major changes, then I will advise against it. I rather suggest that we use the mailing list to raise issues publicly - if there is a dispute, we should discuss it and form a consensus. I am CCing all authors in the mailing list to this conversation to clarify what I am asking for them Hopefully it will accelerate the process.</div><div><br></div><div>7. I added your name and affiliation to the list of contributors, yet did not remove the red color to indicate you have not approved yet. </div><div><br></div><div>8. As for definition of publication - in a sense we are public already - and we maintain the links to the changes made by contributors - however, the intention is to submit somewhere for formal review </div><div><br></div><div>I hope the above compromise is sufficient for you to approve submission. </div><div><br></div><div><br></div><div> Jacob</div><div><br></div><div><br></div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Mar 11, 2021 at 12:54 AM John Gennari <<a href="mailto:gennari@uw.edu">gennari@uw.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p><br>
</p>
<p>Greetings, Jacob. <br>
</p>
<p>I hope that Spring has finally found you in Texas, as it has
appeared here in Seattle. I've just now completed my teaching for
the quarter, and so have had the time to return to this white
paper manuscript. <br>
</p>
<p>In your email, you ask just a few questions; I will answer these,
but also provide some thoughts about the paper as a whole. <br>
</p>
<p>My name for publications & manuscripts is "John H Gennari"
(there are a couple other John Gennari in academia, believe it or
not). My affiliation is "Dep't of Biomedical Informatics and
Medical Education, University of Washington". <br>
</p>
<p>I have no conflicts of interest, and I have no target publication
venue in mind (see also my thoughts at the end). <br>
</p>
<p>You also ask "Do you feel comfortable being listed as a
contributor to the composed version? There are no more changes
expected other than minor grammar corrections or fixing issues
listed with comments." This one is a more challenging question, of
course. <br>
</p>
<p>First, my condolences on taking the lead with such a long list of
potential co-authors. I know from personal experience that getting
agreement or any forward movement with more than about 5 or 6
academicians is a challenging task. It can be done, but certainly
requires patience. <br>
</p>
<p>Next, I definitely agree with the great majority of what the
paper says. It is a huge improvement over what I saw before, and
much of my confusion about the manuscript has been alleviated.
There is one relatively small amendment I would like to suggest,
but I don't believe it changes the meaning or direction of the
paper (see below). <br>
</p>
<p>However, I do have some issues with some of the sentence-level
writing. I see that you say "minor grammar corrections" are yet to
occur, but I found many sentences that seemed weak -- not just a
matter of simple grammatical fixes. In at least a few cases, there
seemed to be some important word omissions, so that the meaning
was not at all clear. <br>
</p>
<p>My concern is that even if I agree with the content, I don't want
my name attached to a manuscript that includes many problematic
sentences. The tenor of your emails made it seem like the
manuscript was almost ready to be submitted somewhere, and that
does not sit comfortably with me. Now perhaps this is largely a
stratagem to get us slow-moving academicians to read and respond
to your emails, but....</p>
<p>As an example of my concerns, the section titled "Missing
annotations in Models" has problems, and perhaps is simply
incomplete. E.g. the last line of p. 14 is "However, despite the
intention, there is a lack of use of annotations: ", and there is
nothing following the colon. The sentence also stands alone, as
its own paragraph. The paragraph at the top of page 15 appears to
have some missing words: "This is particular because..." The next
starts starts "This is also particularly because..." Did you mean
"particularly good"? Or particularly problematic, or....? Or
perhaps you meant "This is also especially because..." ?? But if
that's the meaning, then I'm not sure what the "this" refers to. <br>
</p>
<p>These aren't simple grammatical mistakes -- I literally do not
understand what the intended meaning is. <br>
</p>
<p>The one amendment I would like to suggest begins with the nice
table on p. 8, listing all of the difficulties and potential
solutions. In particular, the cell for "adaptation toward
integration" mentions the SBML-Comp tool. I'm somewhat familiar
with this idea SBML extension, and in fact, Max Neal, Lucian Smith
(the author of SBML-Comp), myself and others (indeed, more than 5
co-authors) have written a paper titled "A Reappraisal of How to
Build Modular, Reusable Models of Biological Systems"
(PloSCompBIo, 2014). <br>
</p>
<p>In the table, it suggests that SBML-Comp is a tool, whereas I
think of it more as an extension to the SBML language. In
contrast, Max and I and others have developed a tool for model
adaptation and integration called SemGen (Bioinformatics, 2019).
It's totally appropriate to mention SBML-Comp, but I really don't
think of it as a tool, and if tools are listed, then I'd like to
ask that the SemGen tool be mentioned. If appropriate, I could
also write a sentence or two summarizing the 2014 PLoSCompBio
publication. <br>
</p>
<p>Finally, I would like to add that (as you implied) the paper is
now <b>quite</b> long. As happens with multiple authors, I think
there are places that seem a bit redundant, and I think much could
be reduced from the manuscript without loss. As an example, I did
not find the section at the end on "Open Discussion Issues" to be
useful, nor well-connected to the rest of the manuscript. <br>
</p>
<p>Of course, matters of length are always partially mediated by the
target venue for publication. If by "publication", you simply mean
publication on the IMAG website, then I suppose there would be no
imposed limits. But brevity is often good. <br>
</p>
<p>The COMBINE HARMONY meeting is in less than two weeks (March
22-26). Jon Karr, myself, and Sheriff Rahuman at the least, will
be presenting and busy that week. I also note from the program
that Henning Hermjacob will be giving a brief talk on
"ModelXchange -- Status update and Data Invitation". Might I ask
that we delay any idea of trying to finalize this manuscript until
after this meeting? For me, at least, the meeting might impact how
I think about modularity, multi-scale modeling, and our efforts
and supporting reproducibility. <br>
</p>
<p>I hope you don't find this email too long and annoying. As I
mentioned, I do know that it can be challenging to work with many
co-authors at once. I'd also be happy to iterate further on the
text, if that would be helpful at this stage.<br>
</p>
<p>-John Gennari<br>
</p>
<p>ps: <br>
</p>
<p>Here is the full citation information for the two papers I
mention above: <br>
</p>
<p>Neal ML, Thompson CT, Kim KG, James RC, Cook DL, Carlson BE, and
Gennari JH (2019). SemGen: a tool for semantics-based annotation
and composition of biosimulation models. Bioinformatics.
doi:10.1093/bioinformatics/bty829</p>
<p>Neal ML, Cooling MT, Smith LP, Thompson CT, Sauro HM, Carlson BE,
Cook DL, Gennari JH (2014). A reappraisal of how to build modular,
reusable models of biological systems. PLoS Computational Biology.
doi: 10.1371/journal.pcbi.1003849<br>
</p>
<p><br>
</p>
<p>
</p>
<p class="MsoNormal" style="margin:0in 0in 4pt 18.7pt"><span style="font-family:Arial,sans-serif;background:yellow"><span></span></span><span style="font-family:Arial,sans-serif;background:yellow"><br>
</span><span style="font-family:Arial,sans-serif;background:yellow"></span></p>
<p></p>
<p><br>
</p>
<div>On 3/4/2021 1:46 PM, Jacob Barhak
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Greetings to all the white paper contributors:
<div><br>
</div>
<div>Jonathan Karr<br>
Rahuman Sheriff<br>
James Osborne<br>
Gilberto Gonzalez Parra<br>
Eric Forgoston<br>
Ruth Bowness<br>
Yaling Liu<br>
Robin Thompson<br>
Winston Garira<br>
Jacob Barhak <br>
John Rice <br>
Marcella Torres<br>
John Gennari<br>
Hana M. Dobrovolny <br>
Tingting Tang<br>
William Waites<br>
James Glazier<br>
James R Faeder<br>
<div>
<div><br>
</div>
<div>If you contributed text to the white paper and not on
this list, please let me know as soon as possible - I did
my best to assemble all contributors and want to make sure
no one was missed by mistake. </div>
<div><br>
</div>
<div>Following the reopening, the white paper grew in size.
It is now about 29 pages and 18 contributors. You will
find it here:</div>
<div><a href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing" target="_blank">https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing</a><br>
</div>
<div><br>
</div>
<div>I suggest closing the paper and going again through the
formal approval process so that the paper can be submitted
to some publisher.</div>
<div><br>
</div>
<div>I will ask that all contributors approve the paper - so
if you contributed I expect an email from you with the
following elements:</div>
<div><br>
</div>
<div>1. Do you feel comfortable being listed as a
contributor to the composed version? There are no more
changes expected other than minor grammar corrections or
fixing issues listed with comments. I will need approval
from all contributors to move forward and since there are
many of you, please send confirmation as soon as
possible. </div>
<div><br>
</div>
<div>2. What is your affiliation so I can add it at the
end. <br>
<br>
3. If you have a conflict of interest, please report it so
I can add it to the paper. If you are unsure, please
download the form from this link <a href="http://icmje.org/downloads/coi_disclosure.zip" target="_blank">http://icmje.org/downloads/coi_disclosure.zip</a>
and then fill in the questions and press the generate
button - it will create the COI disclosure text for you.</div>
<div><br>
</div>
<div>4. If you have a target venue in mind for the paper,
please suggest - we will pick one with consensus that
everyone is comfortable with. </div>
<div><br>
</div>
<div>I will ask those who approved the paper before to look
at the changes since the day of approval - we added around
4 pages of text and authors should be aware of.</div>
<div><br>
</div>
<div>For all those who wanted to add material and could not
manage, I apologize - yet at this point it seems we are
refining the ideas and not contributing new ones and it
was open for a while and we need to move on.</div>
<div><br>
</div>
<div>I look forward to your responses.</div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Feb 25, 2021 at 4:29
PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Greetings subgroups,<br>
<div><br>
</div>
<div>James Glazier the working group lead, indicated that
the white paper deadline of tomorrow is flexible, so it is
possible to get additional contributions to the white
paper.</div>
<div><br>
</div>
<div>Therefore I will ask anyone who wanted to contribute
and did not have the chance to contribute to the paper
until the end of the weekend.</div>
<div>Please send me an email to gain access - I will
redacted you to the correct draft. Here is again the link
to the integrated version:<br>
</div>
<div><a href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing" target="_blank">https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing</a><br>
</div>
<div><br>
</div>
<div>Many of you contributed already and some even approved
this assembled manuscript - I asked those who have not
approved already to wait a few more days before
reviewing the paper so that they can approve the final
version next week.</div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
<div><br>
</div>
<div> </div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sat, Feb 20, 2021 at
3:59 AM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Greetings subgroups,
<div><br>
</div>
<div>As promised the merging of both papers have
started. </div>
<div><br>
</div>
<div>Here are some technicalities:</div>
<div><br>
The title of the jint white paper will be:</div>
<div>Model Integration in Computational Biology: the
Role of Reproducibility, Credibility and Utility<br>
<br>
The author of the paper will be:</div>
<div>Multiscale Modeling and Viral Pandemics Working
Group </div>
<div><br>
I looked through all the edit list on the paper and
found the following contributors:<br>
</div>
<div>Jonathan Karr<br>
Rahuman Sheriff<br>
James Osborne<br>
Gilberto Gonzalez Parra<br>
Eric Forgoston<br>
Ruth Bowness<br>
Yaling Liu<br>
Robin Thompson<br>
Winston Garira<br>
Anonymous contributor January 25, 2:13 PM</div>
<div>Jacob Barhak<br>
</div>
<div>John Rice <br>
</div>
<div><br>
</div>
<div>The Anonymous contributor on January 25, 2:13 PM
added the words: ". There are also challenges in
gaining testable insight. Are they truly necessary? ".
. However, unless the contributor identifies
themselves, I cannot add their name and may remove
this sentence since it seems misplaced and not
attributed to any person.</div>
<div> </div>
<div>If I missed any contributor, please let me know so
I can add the person to the list of contributors. I
just looked at the changes history on the document and
pulled names - if anyone added text using an account
by someone else, let me know. </div>
<div><br>
</div>
<div>Also, I will wait for a couple of more days for any
last minute contributions. I will ask for anyone who
wanted to contribute and did not have a chance to edit
the papers directly over the weekend. I will do my
best to integrate changes done over the weekend, yet I
cannot guarantee adding any more changes - we had
enough time to make those edits and we need to wrap
things up at some point. </div>
<div><br>
</div>
<div>I will send the link to the combined draft paper
once it is in good shape for approval. <br>
</div>
<div><br>
</div>
<div>I will try my best to harmonize all contributions
and maintain flow. Yet there are a lot of discussions
and open end issues left, so I am not sure how
practical it is. </div>
<div><br>
</div>
<div>If anyone wants to help editing, let me know. </div>
<div><br>
</div>
<div>Hopefully you will find the final product in good
shape. </div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Feb 12, 2021
at 10:26 AM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Greetings to the model reproducibility,
credibility and standardization and integration
subgroups
<div><br>
</div>
<div>
In the joint meeting of the groups we discussed
the papers and ideas behind the merge as well as
their own contributions to the working group and
paper. <br>
<div><br>
</div>
<div>It was decided unanimously to merge the two
white papers together. </div>
<div><br>
</div>
<div>The white paper drafts are in good form
currently and include a lot of information. You
can find them in these links:</div>
<div><br>
</div>
<div><a href="https://docs.google.com/document/d/1voUSrSpv3AZlC1T-BLa3W4wzHQ5vEdJCVrBbwMUTDiQ/edit?usp=sharing" target="_blank">https://docs.google.com/document/d/1voUSrSpv3AZlC1T-BLa3W4wzHQ5vEdJCVrBbwMUTDiQ/edit?usp=sharing</a></div>
<div><br>
<a href="https://docs.google.com/document/d/1cqwXAjBWEiJZ1tUBnf66QVHdHd2fKq_W0py7t4PNVLo/edit?usp=sharing" target="_blank">https://docs.google.com/document/d/1cqwXAjBWEiJZ1tUBnf66QVHdHd2fKq_W0py7t4PNVLo/edit?usp=sharing</a><br>
</div>
<div><br>
</div>
<div>The group did not reach a conclusion on the
title of the joint paper. Suggestions for
the title are welcome. </div>
<div><br>
</div>
<div>Beyond what was discussed in the meeting I
would like to add the following: </div>
<div><br>
</div>
<div>Since the deadline for the white paper is Feb
26th - it is suggested that all contributors who
want to join the author list of the white paper
will make edits until Feb 19th in the respective
papers. This will allow time to merge the papers
together and send it to both lists. </div>
<div><br>
</div>
<div>Unless someone else volunteers to help merge,
I will personally start the merge on Feb 20th,
so contributions to the text after that date may
not be merged. Individuals who wish to be in the
author list should contribute text before that
date and preferably write their name near the
contributed text. </div>
<div><br>
</div>
<div>I personally look forward to more feedback
and contributions. </div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
</blockquote>
</div>
</blockquote>
</div>
</blockquote>
</div>
</blockquote>
</div>
</blockquote></div>