[Vp-reproduce-subgroup] Recap from joint meeting regarding the white paper
John Gennari
gennari at uw.edu
Thu Mar 18 22:45:18 PDT 2021
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
> <mailto: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
>> <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
>> <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 <mailto: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
>> <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 <mailto: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 <mailto: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/1voUSrSpv3AZlC1T-BLa3W4wzHQ5vEdJCVrBbwMUTDiQ/edit?usp=sharing>
>>
>> https://docs.google.com/document/d/1cqwXAjBWEiJZ1tUBnf66QVHdHd2fKq_W0py7t4PNVLo/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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