[Vp-integration-subgroup] Recap from joint meeting regarding the white paper

[Jonathan Karr]

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.

Regards,
Jonathan

On Fri, Mar 19, 2021 at 1:45 AM John Gennari <gennari at uw.edu> wrote:

> Jacob:
>
> 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.
>
> ************
>
> 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.
>
> Next, for the citation G2 (Neal, et al, 2019), please insert the following
> text into p. 13. New text is indicated in italics:
>
> ...One tool is SBML-comp, but it i's cumbersome and few tools support it. *Another
> tool is SemGen [G2], but it focuses on finding mappings between similar
> models. *To the point here, *both tools are *designed to compose models
> that weren't intended to...."
>
> ************
>
> 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."
>
> I'm going to tease this question apart a bit.
>
> First, I'm happy to be a contributor who agrees with the overarching ideas
> expressed in this document.
>
> 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.
>
> 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.
>
> 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.
>
> -John Gennari
>
>
> On 3/11/2021 12:29 AM, Jacob Barhak wrote:
>
> Thanks John,
>
> 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.
>
> 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.
>
> The agreement should be at the level of good enough for submission - not
> final product.
>
> 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?
>
> 1. I fixed the text issue in pages 14-15 you mentioned - those are minor -
> check the version history for recent changes.
>
> 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.
>
> 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.
>
> 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.
>
> 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.
>
> 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.
>
> 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.
>
> 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
>
> I hope the above compromise is sufficient for you to approve submission.
>
>
>                     Jacob
>
>
>
>
>
> On Thu, Mar 11, 2021 at 12:54 AM John Gennari <gennari at uw.edu> wrote:
>
>>
>> Greetings, Jacob.
>>
>> 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.
>>
>> In your email, you ask just a few questions; I will answer these, but
>> also provide some thoughts about the paper as a whole.
>>
>> 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".
>>
>> I have no conflicts of interest, and I have no target publication venue
>> in mind (see also my thoughts at the end).
>>
>> 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.
>>
>> 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.
>>
>> 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).
>>
>> 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.
>>
>> 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....
>>
>> 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.
>>
>> These aren't simple grammatical mistakes -- I literally do not understand
>> what the intended meaning is.
>>
>> 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).
>>
>> 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.
>>
>> Finally, I would like to add that (as you implied) the paper is now
>> *quite* 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.
>>
>> 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.
>>
>> 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.
>>
>> 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.
>>
>> -John Gennari
>>
>> ps:
>>
>> Here is the full citation information for the two papers I mention above:
>>
>> 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
>>
>> 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
>>
>>
>>
>>
>> On 3/4/2021 1:46 PM, Jacob Barhak wrote:
>>
>> Greetings to all the white paper contributors:
>>
>> Jonathan Karr
>> Rahuman Sheriff
>> James Osborne
>> Gilberto Gonzalez Parra
>> Eric Forgoston
>> Ruth Bowness
>> Yaling Liu
>> Robin Thompson
>> Winston Garira
>> Jacob Barhak
>> John Rice
>> Marcella Torres
>> John Gennari
>> Hana M. Dobrovolny
>> Tingting Tang
>> William Waites
>> James Glazier
>> James R Faeder
>>
>> 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.
>>
>> Following the reopening, the white paper grew in size. It is now about 29
>> pages and 18 contributors. You will find it here:
>>
>> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>>
>> I suggest closing the paper and going again through the formal approval
>> process so that the paper can be submitted to some publisher.
>>
>> I will ask that all contributors approve the paper - so if you
>> contributed I expect an email from you with the following elements:
>>
>> 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.
>>
>> 2. What is your affiliation so I can add it at the end.
>>
>> 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
>> http://icmje.org/downloads/coi_disclosure.zip and then fill in the
>> questions and press the generate button - it will create the COI disclosure
>> text for you.
>>
>> 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.
>>
>> 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.
>>
>> 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.
>>
>> I look forward to your responses.
>>
>>                 Jacob
>>
>>
>>
>> On Thu, Feb 25, 2021 at 4:29 PM Jacob Barhak <jacob.barhak at gmail.com>
>> wrote:
>>
>>> Greetings subgroups,
>>>
>>> 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.
>>>
>>> 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.
>>> 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:
>>>
>>> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>>>
>>> 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.
>>>
>>>            Jacob
>>>
>>>
>>>
>>>
>>>
>>> On Sat, Feb 20, 2021 at 3:59 AM Jacob Barhak <jacob.barhak at gmail.com>
>>> wrote:
>>>
>>>> Greetings subgroups,
>>>>
>>>> As promised the merging of both papers have started.
>>>>
>>>> Here are some technicalities:
>>>>
>>>> The title of the jint white paper will be:
>>>> Model Integration in Computational Biology: the Role of
>>>> Reproducibility, Credibility and Utility
>>>>
>>>> The author of the paper will be:
>>>> Multiscale Modeling and Viral Pandemics Working Group
>>>>
>>>> I looked through all the edit list on the paper and found the following
>>>> contributors:
>>>> Jonathan Karr
>>>> Rahuman Sheriff
>>>> James Osborne
>>>> Gilberto Gonzalez Parra
>>>> Eric Forgoston
>>>> Ruth Bowness
>>>> Yaling Liu
>>>> Robin Thompson
>>>> Winston Garira
>>>> Anonymous contributor January 25, 2:13 PM
>>>> Jacob Barhak
>>>> John Rice
>>>>
>>>> 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.
>>>>
>>>> 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.
>>>>
>>>> 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.
>>>>
>>>> I will send the link to the combined draft paper once it is in good
>>>> shape for approval.
>>>>
>>>> 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.
>>>>
>>>> If anyone wants to help editing, let me know.
>>>>
>>>> Hopefully you will find the final product in good shape.
>>>>
>>>>               Jacob
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Fri, Feb 12, 2021 at 10:26 AM Jacob Barhak <jacob.barhak at gmail.com>
>>>> wrote:
>>>>
>>>>> Greetings to the model reproducibility, credibility and
>>>>> standardization and integration subgroups
>>>>>
>>>>> 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.
>>>>>
>>>>> It was decided unanimously to merge the two white papers together.
>>>>>
>>>>> The white paper drafts are in good form currently and include a lot of
>>>>> information. You can find them in these links:
>>>>>
>>>>>
>>>>> https://docs.google.com/document/d/1voUSrSpv3AZlC1T-BLa3W4wzHQ5vEdJCVrBbwMUTDiQ/edit?usp=sharing
>>>>>
>>>>>
>>>>> https://docs.google.com/document/d/1cqwXAjBWEiJZ1tUBnf66QVHdHd2fKq_W0py7t4PNVLo/edit?usp=sharing
>>>>>
>>>>> The group did not reach a conclusion on the title of the joint paper.
>>>>> Suggestions for the title are welcome.
>>>>>
>>>>> Beyond what was discussed in the meeting I would like to add the
>>>>> following:
>>>>>
>>>>> 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.
>>>>>
>>>>> 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.
>>>>>
>>>>> I personally look forward to more feedback and contributions.
>>>>>
>>>>>              Jacob
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
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