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

[Jacob Barhak]

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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