<div dir="ltr">Hi Jacob and all,<div><br></div><div>The general idea of the article is very good. Probably, each of us would have some personal viewpoints but I think in general the topic is very important and broad. The article covers several topics in a broad sense as should be in a first general paper.</div><div>As mentioned before by Jacob, we couldn't add additional paragraphs to the manuscript to avoid delays. That is one strategy that might be good or not. I think we can move forward and as Jacob has mentioned the reviewers would suggest some changes and particular explanations plus more classical references. One aspect that I wanted to add was the one related to identifiability of parameters which is a crucial aspect in every mathematical model, and that is very related to credibility. We can wait until we get the feedback and then decide what to add depending on the questions. </div><div><br></div><div>Best,</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">***************************************************************************</div><div dir="ltr">Gilberto C. Gonzalez-Parra, <span style="color:rgb(0,0,0);font-family:"Helvetica Neue",Helvetica,Arial,"Lucida Grande",sans-serif,serif,EmojiFont;font-size:13px">Ph.D in Applied Mathematics.</span></div><div dir="ltr"><font color="#000000" face="Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif, serif, EmojiFont"><span style="font-size:13px">Faculty of the </span></font>Mathematics Department<div><div>New Mexico Tech, NM, USA.</div></div><div>****************************************************************************</div></div></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Mar 19, 2021 at 8:27 AM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com">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">Thanks Winston,<div><br></div><div>You are now marked as approved. However, you will have to note if you have any conflict of interest. </div><div><br></div><div>Winston, your suggestion to add more text comes very late, most authors approved the text and those few lines of text and the reference, as important as they are, will probably not change the paper, yet if you add your text and all other contributors who want to add only one more line get their will, the paper will be delayed significantly and we will have to do another approval round.</div><div><br></div><div>Since we still have to go through several stages before publication so I suggest
that you keep this addition towards a future revision. There are times where additions become subtractions - I believe we are in that time.</div><div><br></div><div>Nevertheless, your text seems to correspond to the willingness of many in the working group to work to better define integration/composition - please see Williams email. We had support form William, James Glazier, and yourself to better define integration/composition - perhaps it is an opening for another paper focusing on those topics alone. You are welcome to start another discussion on this mailing list and develop ideas towards another paper. Or you can wait to see if this paper will reopen after review to add new ideas. In any case, I thank you for your support.</div><div><br></div><div> Jacob</div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Mar 19, 2021 at 7:47 AM Winston Garira <<a href="mailto:Winston.Garira@univen.ac.za" target="_blank">Winston.Garira@univen.ac.za</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">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<span style="font-family:Arial,Helvetica,sans-serif;font-size:12pt">Hi Jacob,</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif">I am happy to be listed as a contributor and my affiliation is given at the end of this message. I would like to suggest that minor changes should be introduced to the integration of
scales section of this paper. I have been working on model integration for some time now. I suggest that minor changes should be incorporated that convey a consolidated idea on model integration. The integration of scales </span><span style="font-size:14pt;font-family:Arial,sans-serif"><span style="color:black;font-size:12pt;font-family:Arial,Helvetica,sans-serif">
</span></span><span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif">is one of the grand challenges in the development of multiscale models. There are two forms of integration/linkage</span><span style="font-size:14pt;font-family:Arial,sans-serif"><span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif">
</span></span><span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif">of scales which should be emphasized in the development of multiscale models: [a.] Biological integration/linkage</span><span style="font-size:14pt;font-family:Arial,sans-serif"><span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif">
</span></span><span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif">of scales through exchange of organisms implicated in disease dynamics across multiple scales. </span><span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif">
[b.]</span><span style="font-size:14pt;font-family:Arial,sans-serif"><span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif">
</span></span><span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif">Mathematical/quantitative integration/linkage</span><span style="font-size:14pt;font-family:Arial,sans-serif"><span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif">
</span></span><span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif">of scales through mathematical methods that represent</span><span style="font-size:14pt;font-family:Arial,sans-serif"><span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif">
</span></span><span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif">biological integration/linkage</span><span style="font-size:14pt;font-family:Arial,sans-serif"><span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif">
</span></span><span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif">of scales. </span><span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif"><span style="font-size:12pt;line-height:normal;font-family:Arial,Helvetica,sans-serif">This
second aspect of model integration involves </span><span style="font-size:12pt;line-height:normal;font-family:Arial,Helvetica,sans-serif"> finding appropriate quantitative (mathematical, statistical, computational, algorithmic, etc.) ways of representing
the biological mechanisms of linkage between the scales of an infectious disease system and has hindered progress in the development of multiscale models. I am aware that at this stage no more new references can be added but the following reference may be
found useful in guiding such a consolidation of the model integration section.</span></span></div>
<span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif"><span style="font-size:12pt;line-height:normal;font-family:Arial,Helvetica,sans-serif">
<p class="MsoNormal" style="margin:0in 0in 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif">
<span style="font-size:14pt;font-family:Arial,sans-serif"><br>
</span></p>
<p class="MsoNormal" style="margin:0in 0in 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif">
<i><span style="font-size:14pt;font-family:Arial,sans-serif">Garira, W. (2020). The research and development process for multiscale models of infectious disease systems. PLoS computational biology, 16(4), e1007734.<u></u> <u></u></span></i></p>
</span></span>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif"><span style="font-size:12pt;line-height:normal;font-family:Arial,Helvetica,sans-serif"><br>
</span></span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif"><span style="font-size:12pt;line-height:normal;font-family:Arial,Helvetica,sans-serif"><br>
</span></span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif"><span style="font-size:12pt;line-height:normal;font-family:Arial,Helvetica,sans-serif"></span></span><span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif"><span style="font-size:12pt;line-height:normal;font-family:Arial,Helvetica,sans-serif">
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif">
<b><span style="font-family:Arial,sans-serif">Winston Garira, PhD<u></u> <u></u></span></b></p>
</span></span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif"><span style="font-size:12pt;line-height:normal;font-family:Arial,Helvetica,sans-serif">
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif">
<b><span style="font-family:Arial,sans-serif">DEPARTMENT OF MATHEMATICS AND APPLIED MATHEMATICS<u></u> <u></u></span></b></p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif">
<b><span style="font-family:Arial,sans-serif">Modelling Health and Environmental Linkages Research Group (MHELRG)<u></u> <u></u></span></b></p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif">
<b><span style="font-family:Arial,sans-serif">University of Venda, Private Bag X5050, Thohoyandou 0950, South Africa.
<u></u><br>
<u></u></span></b></p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif">
<b><span style="font-family:Arial,sans-serif">Email(1):
<u><span style="color:blue"><a href="mailto:winston.garira@univen.ac.za" target="_blank">winston.garira@univen.ac.za</a></span></u>, Email(2):
<u><span style="color:blue"><a href="mailto:wgarira@gmail.com" target="_blank">wgarira@gmail.com</a></span></u></span></b><span style="font-family:Arial,sans-serif"><u></u> <u></u></span></p>
<br>
</span></span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
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<span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif"><span style="font-size:12pt;line-height:normal;font-family:Arial,Helvetica,sans-serif"><br>
</span></span><span style="font-size:14pt;font-family:Arial,sans-serif"><u></u><span style="font-size:12pt;font-family:Arial,Helvetica,sans-serif"></span><u></u></span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
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<div id="gmail-m_5076700322863518384gmail-m_-8857324022475283457appendonsend"></div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_5076700322863518384gmail-m_-8857324022475283457divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>><br>
<b>Sent:</b> Friday, 19 March 2021 12:25<br>
<b>To:</b> Jonathan Karr <<a href="mailto:jonrkarr@gmail.com" target="_blank">jonrkarr@gmail.com</a>><br>
<b>Cc:</b> John Gennari <<a href="mailto:gennari@uw.edu" target="_blank">gennari@uw.edu</a>>; <a href="mailto:vp-integration-subgroup@lists.simtk.org" target="_blank">vp-integration-subgroup@lists.simtk.org</a> <<a href="mailto:vp-integration-subgroup@lists.simtk.org" target="_blank">vp-integration-subgroup@lists.simtk.org</a>>; <a href="mailto:vp-reproduce-subgroup@lists.simtk.org" target="_blank">vp-reproduce-subgroup@lists.simtk.org</a> <<a href="mailto:vp-reproduce-subgroup@lists.simtk.org" target="_blank">vp-reproduce-subgroup@lists.simtk.org</a>>; Faeder, James R <<a href="mailto:faeder@pitt.edu" target="_blank">faeder@pitt.edu</a>>; Winston Garira <<a href="mailto:Winston.Garira@univen.ac.za" target="_blank">Winston.Garira@univen.ac.za</a>>;
William Waites <<a href="mailto:wwaites@ieee.org" target="_blank">wwaites@ieee.org</a>>; Bruce Shapiro <<a href="mailto:shapirobg@gmail.com" target="_blank">shapirobg@gmail.com</a>>; Laubenbacher,Reinhard <<a href="mailto:reinhard.laubenbacher@medicine.ufl.edu" target="_blank">reinhard.laubenbacher@medicine.ufl.edu</a>>; James Glazier <<a href="mailto:jaglazier@gmail.com" target="_blank">jaglazier@gmail.com</a>><br>
<b>Subject:</b> Re: Recap from joint meeting regarding the white paper</font>
<div> </div>
</div>
<div>
<div dir="ltr">Thanks John, Thanks Jonathan,
<div><br>
</div>
<div>John, first thanks for supporting the paper and for fixing the reference issue - I added your minor changes to the current version. <br>
<div><br>
</div>
<div>However, both you and Jonathan put me in a difficult position. You see, I invited you both as experts to contribute your knowledge to increase the potency of the claims in the paper. I did this in a timely manner according to timelines that were given
by the working group leads. You both contributed and I did my best to integrate your texts with many others who contributed. My preferences in the integration process were to keep things as open as possible while preserving the texts contributed as much as
possible. I believe each contributor can find their words with very minor changes in the text - I really tried not to change anything unless absolutely necessary to keep flow.</div>
<div><br>
</div>
<div>To proceed forward and send this to publication, I need approval of all contributors to legally sign the copyright transfer. If I do not get your approval it is technically plagiarism. John, in your position, you must be aware of this and I am happy you
decided to approve submission without your name in the authors list - since your declaration was made publicly, I see this as an equivalent to copyright transfer so that group can proceed to submission without the group removing texts you contributed and going
through another approval round. Please correct me if I am wrong and you have any copyright claims on any text you contributed.</div>
<div><br>
</div>
<div>I respect John's wishes to be removed from the list of authors - I removed you despite my wishes to keep you in. You see, the paper is about 23 pages and we had 18 contributors - this means that the contribution of each author is limited and none of the
authors really shape the entire paper as you want to - some authors like Jonathan contributed more text and some less. Yet each had some ideas they contributed. The approval process we are going through is to make sure that each author knows each of the other
contributions and has no objections. In simple words, each author is ok with defending the ideas in the paper and believes there are benefits in publishing it and being associated with the paper. If any contributor thinks they cannot be associated with the
paper under these terms, then they should not approve. And if you think something is wrong or incorrect - for sure everyone should know about it before we submit. </div>
<div><br>
</div>
<div>Just to give an example, I had a strong opinion on the use of the term "standard" and raised this topic many times in this working group - today I would not be willing to be an author on a paper that lists some specs as a standard without going through
the proper standardization process. However, I am more than willing to compromise if another term is used to describe good work in a standardization process that was not completed. This is my level of compromise on this one topic and each one of the contributors
has to decide on their level of compromise with many topics listed in the paper. </div>
<div><br>
</div>
<div>To submit a paper to a 3rd party publisher and have your name listed as an author I need to make sure you are ok with the compromises made when assembling the paper. </div>
<div><br>
</div>
<div>John is unwilling to make the compromise to be listed as an author - I respect this, yet personally think he should reconsider - John your contributions on annotations are important and were invited on purpose and you can help us defend some ideas in
the paper if challenged. </div>
<div><br>
</div>
<div>Jonathan, you already approved, in my mind it meant that you made the compromise that allowed this paper to proceed to the next stage. If this is incorrect and you are uncomfortable with being associated with the text, please withdraw your approval and
let us know if you are ok if your substantial text contributions can be used without your name in the contributors list. </div>
<div><br>
</div>
<div>I also want you to consider one more thing. Time is an important factor you should weigh in your decision. Rapid publication of the work will have a faster impact. Perfecting work beyond some point in time has a negative effect since flow of ideas are
delayed in the name of perfection. Also what is perfect for one person may not be perfect to another and the more contributors there are the larger the chance of disagreement which will delay things further - sometimes indefinitely. Under those conditions,
you should ask yourself this question: "is the release of this manuscript serve more good if published early, or are changes to contribute are worth the damage of delay and need for additional rounds of approvals after more change?" </div>
<div><br>
</div>
<div>Also remember that if we submit to a peer review journal, there will most probably be a request for changes - I saw only once a paper that was not returned for changes and I blame the review process. So chances are that even the version we have will have
to go through some changes - so the question is if you are ok with submitting this version knowing there will be changes?</div>
<div><br>
</div>
<div>The work we accomplished in the working group with this white paper draft just started. There will be plenty more work in the future if we decide to persist. John, you are more than welcome to join the mailing lists and register yourself with the working
group leads this will help you keep track of our activities and participate in them. I believe you can contribute a lot with your expertise on annotations. In fact, I think you should speak with the working group leaders to present a webinar on annotations
at the Thursday Webinar series. You are also more than welcome to change your mind and rejoin the contributor list - I will gladly add you. I made sure the working group leads are CCd to this message to make it easier to contact them.</div>
<div><br>
</div>
<div>Jonathan, I hope your previous approval stands after reading this message.</div>
<div><br>
</div>
<div>I would really appreciate your future participation.</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>
</div>
</div>
<br>
<div>
<div dir="ltr">On Fri, Mar 19, 2021 at 1:05 AM Jonathan Karr <<a href="mailto:jonrkarr@gmail.com" target="_blank">jonrkarr@gmail.com</a>> wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">I agree with John's sentiments. I support the overarching ideas in the document. Toward that end, I'm happy to signal that as a listed contributor. However, I think the manuscript needs polishing for submission to a journal. For example, the
abstract would need to be rephrased for a broader audience.
<div><br>
</div>
<div>Regards,</div>
<div>Jonathan</div>
</div>
<br>
<div>
<div dir="ltr">On Fri, Mar 19, 2021 at 1:45 AM John Gennari <<a href="mailto:gennari@uw.edu" target="_blank">gennari@uw.edu</a>> wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Jacob: <br>
</p>
<p>Thanks for all of your emails. My reply will be in two parts. It seems like the most pressing thing is answer some specific questions that were in the comments addressed to me, including providing text for one of the citations listed (#G2). I will do that
first. Next, you are looking for approval from the 18 people listed at the bottom; I will address that second. I've cc'd all of those that you suggested I do in such correspondence.
<br>
</p>
<p>************<br>
</p>
<p>First, in two spots (p. 10 and p. 14), you ask me to verify if the use of the word "consistent" when talking about standards (or de facto standards) such as SBML is okay. Absolutely, this is fine. I do note that the current text avoids using the word "standard"
at all, and I'm also okay with this. <br>
</p>
<p>Next, for the citation G2 (Neal, et al, 2019), please insert the following text into p. 13. New text is indicated in italics:
<br>
</p>
<p>...One tool is SBML-comp, but it i's cumbersome and few tools support it. <i>Another tool is SemGen [G2], but it focuses on finding mappings between similar models.
</i>To the point here, <i>both tools are </i>designed to compose models that weren't intended to...."<br>
</p>
<p>************</p>
<p>For the approval bit, you write: "Do you feel comfortable being listed as a contributor to the composed version? There are no more changes expected other than minor grammar corrections."</p>
<p>I'm going to tease this question apart a bit. <br>
</p>
<p>First, I'm happy to be a contributor who agrees with the overarching ideas expressed in this document.
<br>
</p>
<p>However, in its current shape, I am not willing to be listed as co-author, even for "just" an initial journal submission. I make a pretty strong distinction between general support of ideas, and willingness to attach my name to a specific piece of text.
As graduate program director, I have to "walk the walk" about the responsibilities of academic authorship.
<br>
</p>
<p>If you want to submit this text to some journal in the near future, I absolutely give you permission to do so without my name. I have not contributed much anyways. However, I would hope that I would continue to be invited to comment on and contribute to
this sort of document. Reproducibility, annotation, and model reuse is definitely my research area, and I would love to continue to help move the field forward.
<br>
</p>
<p>Really, I think that I joined this process very late, and didn't have the opportunity to shape the document early on. Without that kind of opportunity, I don't think that co-authorship is appropriate. If for some reason, you do think that I should be a co-author,
then I would want to provide much more input. This would slow down the whole process (which no one wants). On the other hand, if the whole process slows down for other reasons, then I would be happy to provide more input and feedback about the text.
<br>
</p>
<p>-John Gennari</p>
<p><br>
</p>
<div>On 3/11/2021 12:29 AM, Jacob Barhak wrote:<br>
</div>
<blockquote type="cite">
<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>
<div dir="ltr">On Thu, Mar 11, 2021 at 12:54 AM John Gennari <<a href="mailto:gennari@uw.edu" target="_blank">gennari@uw.edu</a>> wrote:<br>
</div>
<blockquote 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 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><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://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM%2Fedit%3Fusp%3Dsharing&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C6e3cfb981253418c3f4c08d8eac1680a%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637517463711407293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=%2Fq3IFbz52i5mp3yBmApi50tCuRglYyiC7Yu9Um54cJU%3D&reserved=0" 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="https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Ficmje.org%2Fdownloads%2Fcoi_disclosure.zip&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C6e3cfb981253418c3f4c08d8eac1680a%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637517463711417287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=K4PW2IcI%2BKtUlfUWSF3zKED%2B6yd6zJhuquHX3rsWbHc%3D&reserved=0" 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>
<div dir="ltr">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 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://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM%2Fedit%3Fusp%3Dsharing&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C6e3cfb981253418c3f4c08d8eac1680a%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637517463711427282%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=H8FyiaMzgwXcoNmMQSnO2T4xN%2B9eXzssxMXANyqxgZA%3D&reserved=0" 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>
<div dir="ltr">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 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>
<div dir="ltr">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 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://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1voUSrSpv3AZlC1T-BLa3W4wzHQ5vEdJCVrBbwMUTDiQ%2Fedit%3Fusp%3Dsharing&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C6e3cfb981253418c3f4c08d8eac1680a%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637517463711427282%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=nShFKzoIdckH16hr9m8ZsdW6GutaT1D36GjMeeKZ%2F3Q%3D&reserved=0" target="_blank">https://docs.google.com/document/d/1voUSrSpv3AZlC1T-BLa3W4wzHQ5vEdJCVrBbwMUTDiQ/edit?usp=sharing</a></div>
<div><br>
<a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1cqwXAjBWEiJZ1tUBnf66QVHdHd2fKq_W0py7t4PNVLo%2Fedit%3Fusp%3Dsharing&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C6e3cfb981253418c3f4c08d8eac1680a%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637517463711437279%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=t5EkXDnSGGPfYOUYMVzb4n7n%2BdWh1EJj%2B0ycbIvUmIQ%3D&reserved=0" 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>
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_______________________________________________<br>
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</blockquote></div>