[Vp-integration-subgroup] [Vp-reproduce-subgroup] Recap from joint meeting regarding the white paper
Laubenbacher,Reinhard
Reinhard.Laubenbacher at medicine.ufl.edu
Fri Apr 2 04:38:52 PDT 2021
Dear all,
while I am not an author on this manuscript, let me add a thought. What Jacob describes
applies to a contract, but maybe not so much to a grant. Grant deliverables are not spelled
out explicitly and can include things related to the research, such as training students,
organizing workshops, or authoring papers broadly related to the topic of the funded research.
I agree that every author should decide on their own how this work fits with their individual
situation.
Reinhard
Reinhard C. Laubenbacher, Ph.D.
Dean’s Professor of Systems Medicine
Director, Laboratory for Systems Medicine
Division of Pulmonary, Critical Care, and Sleep Medicine
Department of Medicine
University of Florida
________________________________
From: William Waites <wwaites at ieee.org>
Sent: Friday, April 2, 2021 3:21 AM
To: Jacob Barhak <jacob.barhak at gmail.com>
Cc: Rahuman Sheriff <sheriff at ebi.ac.uk>; Bruce Shapiro <shapirobg at gmail.com>; vp-reproduce-subgroup at lists.simtk.org <vp-reproduce-subgroup at lists.simtk.org>; vp-integration-subgroup at lists.simtk.org <vp-integration-subgroup at lists.simtk.org>; Jonathan Karr <jonrkarr at gmail.com>; John Gennari <gennari at uw.edu>; Winston Garira <Winston.Garira at univen.ac.za>; Laubenbacher,Reinhard <Reinhard.Laubenbacher at medicine.ufl.edu>; Faeder, James R <faeder at pitt.edu>
Subject: Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] Recap from joint meeting regarding the white paper
[External Email]
Jacob, I suggest that it is better to let the individual authors decide what is appropriate for them to acknowledge and not second-guess what their situation is. In my case, the local norm is that I should do, regardless of your experience in the university system. In the interests of transparency it is also better to mention any funding that could be relevant.
I am paid on a grant from the MRC to understand the COVID-19 epidemic in a particular part of London. I’m not doing anything at multiple scales, and the grant is not about supporting international efforts to improve the state of the art in computational modelling methodology. However, I am using compositional techniques that are relevant for what the group is doing and dissemination is always a part of research grants. If some idea or technique that I have to develop to do the work that I am paid to do turns out to be useful elsewhere, or helps inform discussion in a working group on viral pandemics, then that is something to include when reporting to them. It shows “impact”, funders like that, it costs nothing, and it’s good for everyone.
-w
> On 1 Apr 2021, at 22:01, Jacob Barhak <jacob.barhak at gmail.com> wrote:
>
> Thanks William,
>
> Since you brought up funding sources, allow me to name a comment.
>
> If you are funded to do exactly the work we did in this white paper, the grant number should be mentioned. However, if you are funded to do some computational modeling work to produce results, then perhaps it will not be appropriate. After all this working group effort is supposed to be a volunteer group. As much as this work is important, I am not aware of anyone being paid to do it, if there is such a person, I would ask them to step up and take more responsibility.
>
> I suspect that only people like Sheriff may have grants targeting reproducibility issues, although I might be wrong.
>
> I know that when I was in the University system, I have to go over all the funding sources once a year and sign a legal declaration that ties the funding sources to the work I did and associated amounts of effort. Those numbers matter since they report how public money is spent. And if public money was spend to produce this white paper - it must be transparent. As far as I know this did not happen, yet I might be wrong and may need correction.
>
> I will let each and every one of you to decide if they need to include their funding source on this white paper - you know what you are funded for. Yet I ask you put this publicly on this mailing list - otherwise it is hard for me to collect all the pieces together.
>
> You should include this with your reference of publication venue.
>
> Jacob
>
>
>
>
>
> On Thu, Apr 1, 2021 at 1:40 PM William Waites <wwaites at ieee.org> wrote:
> I don’t have strong feelings about which journal (I would tend to avoid Elsevier also if we can, but I have no moral objection to PLoS) and am happy to go with the consensus.
>
> We should also collect together the grants and funders that like being acknowledged. MRC grant MR/V027956/1 for me. To be clear, because Jacob asked me off list, I am not funded by that grant or any other to work on this project, but it does pay my salary and it’s polite to acknowledge them.
>
> Cheers,
> -w
>
> > On 1 Apr 2021, at 18:08, Jacob Barhak <jacob.barhak at gmail.com> wrote:
> >
> > Thanks Sheriff,
> >
> > The rest of the collaborators should know we spoke in length and my argument was that delaying publication until every collaborators gets all their edits in is not reasonable and the delay will do more damage than good. We already accumulated enough material to make considerable impact and spending the time on improving the work further will be worse than submitting it and making changes after review.
> >
> > After about an hour and a half discussing changes, I added 2 minor grammatical changes to clarify things:
> > 1. ModeleExchange that we added in the paper is a future project that deals with links to repositories rather than an existing repository- this was clarified - otherwise it would be a factual error.
> > 2. SBML-Comp is a specification rather than a software tool
> >
> >
> > Please note that we will reopen the paper for changes after review.
> >
> > With the approval of all collaborators except for one that wanted to withdraw association and may join ater, we can move on to the question of where to publish the paper.
> >
> > I collected your answers to the question of possible venues and here is the list I compiled for publication alternatives:
> >
> >
> > Jonathan Karr:
> > First, a preprint could be posted to something like Zenodo. Unfortunately, bioRxiv probably won't accept this because it doesn't report new results.
> >
> > For journals, may be Briefings in Bioinformatics. Another possibility is to distill the current document down to a few pages which is suitable for a broader range of journals such as Trends in Biotechnology. The current draft could then become supplementary material to the main, shorter paper.
> >
> >
> >
> > William Waites:
> > I wonder if Journal of the Royal Society Interface might be appropriate:
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__royalsocietypublishing.org_journal_rsif&d=DwIFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=N6qR6fcvXlGPRXLNqPIWehZxLqpmEtIYr3aywr8w_hE&s=q6hVW0vSU8NzGjlo2IjpDpef70Vs8SBXSDkZ-FyT4SE&e=
> >
> >
> >
> > Robin Thompson:
> > PLoS Comp Bio
> >
> >
> > Gilberto Gonzalez-Parra
> >
> > plosone
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.journals.elsevier.com_public-2Dhealth&d=DwIFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=N6qR6fcvXlGPRXLNqPIWehZxLqpmEtIYr3aywr8w_hE&s=6-eiJTe7FRrBoY_W8rqud-5cBmFzJ1id5T21Z2AabBs&e=
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.annualreviews.org_journal_publhealth&d=DwIFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=N6qR6fcvXlGPRXLNqPIWehZxLqpmEtIYr3aywr8w_hE&s=9VVu1DtUwjiCgnjvtyGnuaMU_zbAKhlu1b047Zeagas&e=
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bmj.com_&d=DwIFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=N6qR6fcvXlGPRXLNqPIWehZxLqpmEtIYr3aywr8w_hE&s=3jzF28sJg58U-cV7v5I7L435EQ1cQh_h8Z45CtbVVoo&e=
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.sciencedirect.com_journal_simulation-2Dmodelling-2Dpractice-2Dand-2Dtheory&d=DwIFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=N6qR6fcvXlGPRXLNqPIWehZxLqpmEtIYr3aywr8w_hE&s=iskUMbWTmMmXsv9K6XdoOAlbbjFlu_gLEkys55jfR7U&e=
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.sciencedirect.com_journal_methods&d=DwIFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=N6qR6fcvXlGPRXLNqPIWehZxLqpmEtIYr3aywr8w_hE&s=BU9q_V_Dh-dueJeM6Otvhw0SB2QXBAIk4vmrtKJhdo8&e=
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.annualreviews.org_journal_bioeng&d=DwIFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=N6qR6fcvXlGPRXLNqPIWehZxLqpmEtIYr3aywr8w_hE&s=QzHw7RNxXBulkEcCj-sML3qXeCuQu08TI3vPu42okOM&e=
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__f1000research.com_&d=DwIFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=N6qR6fcvXlGPRXLNqPIWehZxLqpmEtIYr3aywr8w_hE&s=CDW0apOvCyQUXMAlbKiY4dQOTF2JYjq9O7qAt50BRU8&e=
> >
> > James R Faeder:
> > I am an editor at PLOS Computational Biology, where I’m sure it would be well-received, but I would guess that others will want to aim for higher impact, at least initially.
> >
> > James Glazier:
> > iScience, Proc. Roy. Soc. Interface, PLoS Comp. Bio, Bulletin of Mathematical Biology, Bioinformatics.
> >
> > Sheriff:
> > Briefings in Bioinformatic
> >
> >
> > If I missed anything please correct me, I did my best collecting those suggestions from many scattered emails
> >
> > When this effort started at the subgroup meeting, I publicly announced that I will not invest time on anything that gets submitted to a PLOS or an Elsevier Journal - I had bad dealing with those and will not touch a manuscript targeted at those venues. So I would ask those to be taken off the option list. However, I have no preference as to other venues and like the idea of a preprint.
> >
> > I would ask that we try to reach a consensus about the target venue. So please if anyone has an objection to any of the above please let us all know publicly - please do not send me a private email. We will collect objections first to form a shortlist of candidates and then vote on the short list.
> >
> > Once we figure out the target venue I will format the approved manuscript and submit it on behalf of the working group.
> >
> > Hopefully this process seems reasonable.
> >
> > Jacob
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > On Thu, Apr 1, 2021 at 11:36 AM Rahuman Sheriff <sheriff at ebi.ac.uk> wrote:
> > Dear Jacob and all,
> >
> > I approve to be listed as an author and the manuscript could be submitted after some polishing as others suggested; but I would like the points listed in the version below to be addressed in the next revision.
> >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh_edit&d=DwIFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=N6qR6fcvXlGPRXLNqPIWehZxLqpmEtIYr3aywr8w_hE&s=D1g1fqKx_IEbtTh8dRY3QfLQOfvCsWGH4OfhXTfRfwI&e=
> >
> > I had a discussion with Jacob and as he insisted we should move forward soon, so we arrived at this conclusion.
> >
> > Best regards
> > Sheriff
> >
> >
> >
> >
> >> On 22 Mar 2021, at 19:32, Gilberto Gonzalez-Parra <Gilberto.GonzalezParra at nmt.edu> wrote:
> >>
> >> Hi Jacob and all,
> >>
> >> 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.
> >> 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.
> >>
> >> Best,
> >>
> >> ***************************************************************************
> >> Gilberto C. Gonzalez-Parra, Ph.D in Applied Mathematics.
> >> Faculty of the Mathematics Department
> >> New Mexico Tech, NM, USA.
> >> ****************************************************************************
> >>
> >>
> >> On Fri, Mar 19, 2021 at 8:27 AM Jacob Barhak <jacob.barhak at gmail.com> wrote:
> >> Thanks Winston,
> >>
> >> You are now marked as approved. However, you will have to note if you have any conflict of interest.
> >>
> >> 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.
> >>
> >> 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.
> >>
> >> 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.
> >>
> >> Jacob
> >>
> >>
> >>
> >> On Fri, Mar 19, 2021 at 7:47 AM Winston Garira <Winston.Garira at univen.ac.za> wrote:
> >> Hi Jacob,
> >>
> >> 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 is one of the grand challenges in the development of multiscale models. There are two forms of integration/linkage of scales which should be emphasized in the development of multiscale models: [a.] Biological integration/linkage of scales through exchange of organisms implicated in disease dynamics across multiple scales. [b.] Mathematical/quantitative integration/linkage of scales through mathematical methods that represent biological integration/linkage of scales. This second aspect of model integration involves 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.
> >>
> >>
> >> Garira, W. (2020). The research and development process for multiscale models of infectious disease systems. PLoS computational biology, 16(4), e1007734.
> >>
> >>
> >>
> >> Winston Garira, PhD
> >> DEPARTMENT OF MATHEMATICS AND APPLIED MATHEMATICS
> >> Modelling Health and Environmental Linkages Research Group (MHELRG)
> >> University of Venda, Private Bag X5050, Thohoyandou 0950, South Africa.
> >> Email(1): winston.garira at univen.ac.za, Email(2): wgarira at gmail.com
> >>
> >>
> >>
> >>
> >> From: Jacob Barhak <jacob.barhak at gmail.com>
> >> Sent: Friday, 19 March 2021 12:25
> >> To: Jonathan Karr <jonrkarr at gmail.com>
> >> Cc: John Gennari <gennari at uw.edu>; vp-integration-subgroup at lists.simtk.org <vp-integration-subgroup at lists.simtk.org>; vp-reproduce-subgroup at lists.simtk.org <vp-reproduce-subgroup at lists.simtk.org>; Faeder, James R <faeder at pitt.edu>; Winston Garira <Winston.Garira at univen.ac.za>; William Waites <wwaites at ieee.org>; Bruce Shapiro <shapirobg at gmail.com>; Laubenbacher,Reinhard <reinhard.laubenbacher at medicine.ufl.edu>; James Glazier <jaglazier at gmail.com>
> >> Subject: Re: Recap from joint meeting regarding the white paper
> >>
> >> Thanks John, Thanks Jonathan,
> >>
> >> John, first thanks for supporting the paper and for fixing the reference issue - I added your minor changes to the current version.
> >>
> >> 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.
> >>
> >> 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.
> >>
> >> 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.
> >>
> >> 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.
> >>
> >> 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.
> >>
> >> 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.
> >>
> >> 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.
> >>
> >> 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?"
> >>
> >> 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?
> >>
> >> 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.
> >>
> >> Jonathan, I hope your previous approval stands after reading this message.
> >>
> >> I would really appreciate your future participation.
> >>
> >> Jacob
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> On Fri, Mar 19, 2021 at 1:05 AM Jonathan Karr <jonrkarr at gmail.com> wrote:
> >> 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://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1IMEgmdNkx-2DEsnOjGuegpenSIMmKIkK00Lc8Gred3QxM_edit-3Fusp-3Dsharing&d=DwIFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=N6qR6fcvXlGPRXLNqPIWehZxLqpmEtIYr3aywr8w_hE&s=M4rlpikIm4Y_8uvQ56CfqpuYM9SzPxy_9OKFe9Enox8&e=
> >>>>
> >>>> 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__icmje.org_downloads_coi-5Fdisclosure.zip&d=DwIFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=N6qR6fcvXlGPRXLNqPIWehZxLqpmEtIYr3aywr8w_hE&s=dGxzWJUKaZh7UUctSu7yVV0Xthb7aG5yTQmm1FULKrc&e= 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://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1IMEgmdNkx-2DEsnOjGuegpenSIMmKIkK00Lc8Gred3QxM_edit-3Fusp-3Dsharing&d=DwIFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=N6qR6fcvXlGPRXLNqPIWehZxLqpmEtIYr3aywr8w_hE&s=M4rlpikIm4Y_8uvQ56CfqpuYM9SzPxy_9OKFe9Enox8&e=
> >>>>
> >>>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1voUSrSpv3AZlC1T-2DBLa3W4wzHQ5vEdJCVrBbwMUTDiQ_edit-3Fusp-3Dsharing&d=DwIFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=N6qR6fcvXlGPRXLNqPIWehZxLqpmEtIYr3aywr8w_hE&s=gRQO8wbb-Pb6d08HP5dO2f8f5mRSq4pa_JkanaxyHMY&e=
> >>>>
> >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1cqwXAjBWEiJZ1tUBnf66QVHdHd2fKq-5FW0py7t4PNVLo_edit-3Fusp-3Dsharing&d=DwIFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=N6qR6fcvXlGPRXLNqPIWehZxLqpmEtIYr3aywr8w_hE&s=dkIDHxA6i1Abbh3pM2q9cDtYd1Zuvw6oKh8GcbyWir8&e=
> >>>>
> >>>> 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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> >
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