[Vp-reproduce-subgroup] [Vp-integration-subgroup] Paper review and revision check list
John Rice
john.rice at noboxes.org
Thu Dec 30 13:14:06 PST 2021
I like that!
On Dec 30, 2021, at 15:28, sheriff <sheriff at ebi.ac.uk> wrote:
Hi Jacob,
One crude idea for the graphics could be a cartoon of hurdling, where each hurdle corresponds to the one we listed in the table or the dozen challenges version. Under each, we could add a sentence about it and this could be a summary figure.
Probably there are better ideas.
Best
Sheriff
On 2021-12-30 20:18, Jacob Barhak wrote:
> Thanks Sheriff,
>
> You comments would be more helpful within a different thread https://lists.simtk.org/pipermail/vp-integration-subgroup/2021-December/000324.html
>
> I will copy your text there for continuity. I assumed many are on vacation, yet I was trying to buy time in hope some of us are active.
>
> As for a rewrite. We have gone this road before. No one in the group had a solution on how to preserve all the ideas we discussed and represent all contributions. We lost precious time going in that route.
>
> If anyone knows how to solve it, please suggest, yet know that this may be lost effort that may only delay things.
>
> My opinion is that the reviewers will have to weigh the importance of our summary table compared to any other aspect. If they decide against it, there is always another venue. The price is delay.
>
> And Sheriff, frankly, if a publisher will not publish while preserving all ideas, then what value is being served in publishing?
>
> If a reviewer does not like a particular idea, they should argue against it and we will respond, yet a "general rewrite" argument is not sufficient. A good editor should spot it and act accordingly.
>
> The paper is readable, and has a clear summary for those who need it . Any argument against this "not being good enough" requires proof by example - if none can produce this example, then the argument should be shelved.
>
> For now, I ask that others attempt to join this discussion and attempt to fix the issues we still need attention for.
>
> Specifically, if anyone has an idea on more graphics, please suggest a figure. Sheriff, you created our first figure, if you have ideas for another figure, please help here. Otherwise we have some solutions for the review that we can debate.
>
> Thanks for answering during the holiday season and a happy new year.
>
> Jacob
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> On Thu, Dec 30, 2021, 08:42 sheriff <sheriff at ebi.ac.uk> wrote:
> Hi Jacob,
>
> Thanks for leading the discussion.
>
> You may have to wait until early Jan for everyone to get back from the holidays and respond.
>
> Also, I think, it may not be possible to get away without improving the flow and readability of the manuscript.
>
> Here are my comments on model sharing and license
>
> Indeed often models are hard to locate. Hence in our reproducibility study ( Tiwari et al. 2021, https://doi.org/10.15252/msb.20209982), we strongly recommend authors to make their models public, but more specifically through public repositories such as BioModels (https://www.ebi.ac.uk/biomodels). We recommend authors to submit model codes, parameter sets, and simulation conditions needed to reproduce simulation studies.
>
> BioModels provides model curation and annotation service, where the models' reproducibility is assessed and annotated with controlled vocabularies. The BioModels offers sophisticated search engines to search and locate models and model components (https://www.ebi.ac.uk/biomodels/parameterSearch). Overall this will greatly facilitate model reuse.
>
> More importantly, all models are disseminated under the permissive CC0 license in BioModels. This is because it is crucial to openly release the models developed through public funding. Also, curation services done at BioModels are supported by public funding.
>
> Although few users suggested we use CC-BY, we decided to continue with CC0. However, we strongly recommend our users to properly cite the model when reused and most researchers normally do. Also, If a modeler collects and integrates components from several hundred models, it may become difficult to properly acknowledge them all.
>
> Best regards
>
> Sheriff
>
>
>
> On 2021-12-27 10:59, Jacob Barhak wrote:
>
> Greetings Paper contributors,
>
> Especially Alex, Hana, William, and Sheriff should read this since I name them below.
>
> To move things forwards I started editing the paper and am sending an update of our checklist with responses to the reviewers. Please check the list if you think you want to contribute more to the paper - it is open for editing - the time window will close once we answered all reviewers - however, please focus on what reviewers asked for and do nto add anything else - I am restraining myself from adding more otherwise there will be no end to editing.
>
> The answers for the reviews so far are:
>
> 1. We thank reviewer 1 for pointing out the papers - we added those references into the discussion. Especially we thank the reviewer for pointing out the (Viceconti et al., 2019) paper - it is indeed unique in its attempt to classify and quantify model credibility with some good examples. We agree it should be cited in our paper since it is an important step forward.
>
> 2. TBD - Alex will provide an answer to the reviewer - he confirmed he got the message
>
> 3. I suggest that the reviewer will have the following answer to the request to focus on COVID-19 in the title. We thank the reviewer for the suggestion to focus on COVId-19 and put it in the title. However, we intend the paper to cover more than just one disease - in fact we have examples in the paper that span diabetes, heart disease as well as COVID - We did add recent COVID-19 models as the reviewer suggested, yet we would lie to keep the broader approach and keep the title without change.
>
> 4. TBD - I have no idea for more graphics - this is still an open item - please suggest solutions.
>
> 5. The "Contribution to the Field Statement" section was revised. Any contributor is welcome to edit it further.
>
> 6. Regarding a major rewrite I suggest the following answer to the reviewer: "We thank the reviewer for advice to improve the paper readability and indeed the group is aware that there are many ideas presented in the paper - yet this is expected from a large and diverse group that provided contributions. The reviewer should be aware that we made every attempt to keep all the ideas intact and what seems sometimes as noise, is actually a choir where every voice is important. This choire attempts to explain the modeling complexity. We did have attempts to reduce the work to something easier to digest - see the versions we quote in the paper. However, those versions were never approved by all contributors as necessary for publication - this is actually the law. What the reviewer saw was a compromise that keeps all ideas as best we could while providing a summary that allows readers to jump to sections of interest. Specifically table 1 is perhaps the most important artifact in the paper. and do ask the reviewer to weigh the importance of its quick publication. We can spend months on trying to revise the paper and reach agreement, yet this will probably not change the core of the paper and will waste resources on 18 contributors needing to constantly change things. Therefore we ask that the reviewer consider the benefit of releasing this information fast so it will make an impact rather than sending is back to rewrites that will delay impact in the name of style - an agreement among such a large and diverse group has a weight and the discussions around this paper are transparent so that readers can go back and clarify things if needed. " - beyond this response, if someone wants to spend time and improve the introduction without omitting ideas or references other than their own, then please let us know - I am open to suggestions.
>
> 7. The answer above in 6. should answer the reviewer that requested changing the introduction - however, if anyone has another suggestion, I am open.
>
> 8. I modified the specific section that the reviewer asked to address. Reviewer 2 wants additional discussion around the "reproducibility crisis" section and asks a valid question about expectations we should address - ""Computational biomedical modeling... was expected to be less affected by the reproducibility crisis." Is this true, and why would it be so? " - My answer to the reviewer is that unlike biological processes that have random nature and experiments would not repeat if repeated, while computer software should be deterministic and it should be repeatable if designed well. Unfortunately we are not experiencing this promise. If anyone wants to expand the discussion, please feel free to do so.
>
> 9. TBD - See also point 12. below. A discussion was started in this thread: https://lists.simtk.org/pipermail/vp-integration-subgroup/2021-December/000324.html - suggested discussors are William, and Sheriff - yet anyone else is welcome to join and contributes. So far no confirmation or response was recorded.
>
> 10. A discussion was started in this thread: https://lists.simtk.org/pipermail/vp-integration-subgroup/2021-December/000325.html - suggested discussor is Hana, So far no confirmation or response was recorded.
>
> 11. TBD - Reviewer 2 asks that we better handle the section on Data availability and measurement definitions: I think we need to emphasize solutions and separate them from issues that may not be solvable. However, Hana and I wrote most of this section with some text from Alex I believe, so we perhaps should meet and discuss how to improve it - it is indeed long and needs fixing. Ideas from anyone are welcome.
>
> 12. TBD - See - point 9 above - A discussion was started in this thread: https://lists.simtk.org/pipermail/vp-integration-subgroup/2021-December/000324.html - suggested discussors are William, and Sheriff - yet anyone else is welcome to join and contributes. So far no confirmation or response was recorded.
>
> 13. TBD - Reviewer 2 asks to handle the Model Application and Implementation Barriers section. We should decide what to do there, the section may need expansion since the ideas there are solid, yet the section is short so perhaps enhancing it makes better sense. I am open to suggestions.
>
> The revised paper is available in:
>
> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>
> I ask that all contributors interested in making modifications write those ideas on the mailing list so that we can move forward with this paper.
>
> I really hope some of you will use the time before the year ends to advance this.
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>
> Jacob
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> On Mon, Dec 20, 2021 at 5:50 PM Jacob Barhak <jacob.barhak at gmail.com> wrote:
> Thanks Alex,
>
> The paper opened back for editing. If someone really feels they have to edit and they are not on the list - let me know and I will add them to the list of editors. - yet for now - let us form a plan to answer the reviewers and only then touch text again - otherwise this will get out of hand since there are so many of us.
>
> I appreciate your support.
>
> Jacob
>
> On Mon, Dec 20, 2021 at 3:50 PM Alexander Kulesza <alexander.kulesza at novadiscovery.com> wrote:
> Dear Jacob, dear all,
> Yes will take care of 2. and happy to help wherever I can.
> Best
>
> On Sun, 19 Dec 2021 at 03:10, Jacob Barhak <jacob.barhak at gmail.com> wrote:
>
> Greetings to the paper contributors,
>
> You may have seen my other message where I posted the reviews to our paper. I am sending those again below to start a new thread discussing possible revisions.
>
> Here is a checklist for revisions required:
>
> We should discuss the references that reviewer 1 raised and add them as reference
> Reviewer 1 asked for more discussion around V&V40 - I believe Alex added the text there originally - Alex do you think you can address the request of the reviewer?
> Reviewer 1 asked to focus on COVID-19 at the title - I am not sure we wish to limit our scope since many of our ideas are applicable far beyond COVID-19 - I leave it up for discussion in the group on how to address this request by the reviewer
> Reviewer 1 asked for additional graphics - I am unsure how to address this beyond ur current diagram - ideas will help
> We need to check the "Contribution to the field" section for grammar and spelling - if someone can contribute more elegant text - now is the time - I looked over it now and found no issues - yet I may have missed something - this section may have been missed since it was added last and perhaps vetted less than other sections. Also Reviewer 2 asked for grammar corrections, so it is worthwhile proof reading the paper as a whole.
> Reviewer 2 asks for major rewrite to emphasize why the problems are there - I think we should explain that the core of the paper is the table and perhaps emphasize it in the paper beyond what the current text - we also should reply to the reviewer and explain that the paper is composed of contributions from a large group and we made an effort to include every voice in the choir - each of those voices is important and needs to be preserved - hopefully it will convince the reviewer that change we will add will be sufficient
> Reviewer 2 asks to revise the introduction - I believe some changes are possible - yet the introduction includes contributions from many authors - at least 10 - and I fear losing something important someone contributed - if someone has an idea on how to address this reviewer without a painful transformation, please reply to this message.
> Reviewer 2 wants additional discussion around the "reproducibility crisis" section and asks a valid question about expectations we should address - ""Computational biomedical modeling... was expected to be less affected by the reproducibility crisis." Is this true, and why would it be so? " - My answer to the reviewer is that unlike biological processes that have random nature and experiments would not repeat if repeated, while computer software should be deterministic and it should be repeatable if designed well. Unfortunately we are not experiencing this promise - yet I believe the reviewer wants more discussion beyond this section so I am happy to discuss this.
> Reviewer 2- writes: "Models are Hard to Locate: Are the authors suggesting that entire simulation workflows, from model construction to analysis, should be publicly available? At what point does one consider intellectual property? Do the authors advocate for such extensive publishing for all models, or only ones that are intended to be widely re-used? - those are important points we need to discuss - we need to better explain the difficulties we are having when creating models and the reviewer is absolutely correct about expanding the discussion to IP - I suggest we create a thread for this discussion and reference it - I suggest it we merged with the licensing issue that I will address later - there is a strong connection there - the reviewer was very observant and sees the bigger problem. However,we need to eventually distill our discussion to recommendations that will inline.
> Reviewer 2 asks that we fix the unit standardization section - I believe Hana and myself were the largest contributors there - Hana - I will start a discussion on that topic in a separate email where we can publicly discuss how to fix this - others will be welcome to contribute.
> Reviewer 2 asks that we better handle the section on Data availability and measurement definitions: in think we need to emphasize solutions and separate it from issues that may not be solvable. Ideas are welcome.
> Reviewer 2 asks good questions with regards to licensing following our text- I personally have good answers to the reviewer and William and I had some discussion on the topic in this list I suggest we expand this discussion in a separate thread - hopefully William and perhaps others will join the discussion. This discussion should also address the IP issues raised by the reviewer for the "models are hard to locate section."
> Reviewer 2 asks to handle the Model Application and Implementation Barriers section. We should decide what to do there, the section may need expansion since the ideas there are solid, yet the section is short so perhaps enhancing it makes better sense. I am open to suggestions.
>
> Those are the items I located and my suggestions. It seems we need attention from Alex, Hana, myself and william. However, anyone on the list is welcome to participate and suggest changes.
>
> I will start the discussion threads on specific topics. Hopefully we can get it done quickly.
>
> Jacob
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>
> ########### Original Reviews #############
>
> There are 2 reviews - both require major changes. I am copying the relevant text below. If more appear, I will let you know, yet I only got this message today although the reviews are dated a few days ago.
>
> Reviewer 1:
> Recommendation for the Editor: Substantial revision is required
>
> Please list your revision requests for the authors and provide your detailed comments, including highlighting limitations and strengths of the review. If you have additional comments based on Q2 and Q3 you can add them as well.
>
> Karr and co-authors made an interesting and exaustive point about the reproducibility crisis that leads to inability to reuse and integrate models, especially about COVID-19 disease.
> Within the manuscript some typos and missing information are present.
> I'd suggest the authors to revise the entire manuscript especially in terms of the state of the art, revising and updating the most relevant examples of computational models dealing with COVID-19 and in general about some semi-standardised proposals about the pipeline to follow for the verification and validation of model credibility. In particular, the authors failed to mention and cite some major results on in silico modeling about COVID-19 up to now. See for example:
> a."In silico trial to test COVID-19 candidate vaccines: a case study with UISS platform", Russo, G., Pennisi, M., Fichera, E., ...Viceconti, M., Pappalardo, F., BMC Bioinformatics, 2020, 21, 527.
> b. Russo G, Di Salvatore V, Sgroi G, Parasiliti Palumbo GA, Reche PA, Pappalardo F. "A multi-step and multi-scale bioinformatic protocol to investigate potential SARS-CoV-2 vaccine targets" [published online ahead of print, 2021 Oct 5]. Brief Bioinform. 2021;bbab403. doi:10.1093/bib/bbab403.
> Moreover, when the authors mention ASME V&V40 procedure, it could be useful to spend few words about the model credibility pipeline drawn for predictive models in biomedicine, such as the one suggested in "Credibility of in Silico Trial Technologies-A Theoretical Framing", Viceconti, M., Juarez, M.A., Curreli, C., ...Russo, G., Pappalardo, F., IEEE Journal of Biomedical and Health Informatics, 2020, 24(1), pp. 4–13, 8884189.
> For this specific aspect, the authors should talk about "specific question of interest" and not "specific purpose" in the paragraph called "Credibility of Models" to follow in such a way a standardised language.
> Moreover, the authors should refer to COVID-19 also in the title, with a specific mention about the fact that the main topic of model integration in computational biology will be discussed inside the COVID-19 context.
> Furthermore, for the model key concepts such as Reusability-Extensibility-Extractability-Portability the authors should described and outlined through a graphical sketch or visual representation that summarises these key point.
> The authors should also fix some grammar and writing typos present in the "Contribution to the field" section.
>
> a. Is the quality of the figures and tables satisfactory?
> - No
>
> b. Does the reference list cover the relevant literature adequately and in an unbiased manner?
> - No
>
> c. Does this manuscript refer only to published data? (unpublished or original data is not allowed for this article type)
> - Yes
>
> d. Does the review include a balanced, comprehensive, and critical view of the research area?
> - Yes
>
>
>
> Reviewer 2
>
> Please list your revision requests for the authors and provide your detailed comments, including highlighting limitations and strengths of the review. If you have additional comments based on Q2 and Q3 you can add them as well.
>
>
> The article often reads as a stream-of-consciousness account of the discussions that took place but lacks a clear thesis or recommendations. It is not clear what, if anything, the authors are advocating for. It is not always clear why the issues being discussed are problematic, or that they can be reasonably addressed. Some of the issues raised are indeed important and should be discussed, but the paper lacks focus and does not tell a cohesive story. I believe this manuscript requires a major re-write to be suitable for publication. The authors should consider narrowing the scope of the discussion and focusing on a cohesive set of recommendations or open questions. More specifically, I make a few suggestions below:
>
> Major comments
> 1. The introduction is long and repeats itself (e.g., "much less is known about how viral infections spread throughout the body..." is repeated verbatim). It is not clear from the introduction what the main goal of the paper is or why the "reproducibility crisis" is truly a crisis. Why is the discussion of composition and black/white box models relevant to the introduction? Further, this section is subtitled "the promise of modeling", which does not seem to match the content.
> 2. The Reproducibility Crisis: "Computational biomedical modeling... was expected to be less affected by the reproducibility crisis." Is this true, and why would it be so? One would think that more complex models would suffer more from a lack of reproducibility. It may be helpful to define what exactly the "reproducibility crisis" refers to.
> 3. Models are Hard to Locate: Are the authors suggesting that entire simulation workflows, from model construction to analysis, should be publicly available? At what point does one consider intellectual property? Do the authors advocate for such extensive publishing for all models, or only ones that are intended to be widely re-used?
> 4. Unit standardization: The conversion from PFU or TCID50 to individual virions is likely to differ across viruses – are the authors focused on COVID here? Are the authors advocating for a standard conversion factor? It is not clear what the purpose of this discussion is. As the authors mention, different scales require different units. Even at a single scale, different models may require different units for numerical reasons. It is not clear what the authors are advocating for here.
> 5. Data availability and measurement definitions: This section seems to outline limitations of available data, but again makes no recommendations or proposed solution to any of the issues raised. Is this the intention? Most of the issues raised here reflect limitations of experimental science or data privacy, which likely cannot be meaningfully addressed by the modeling community.
> 6. Models are Not Consistently Licensed...: Are the authors implying here that all modeling work should be published with no rights reserved? Is it reasonable to expect modelers to make their work freely usable by others for profit? Is it reasonable for institutions to allow this? How much does this really contribute to reproducibility and utility?
> 7. Model Application and Implementation Barriers: This section seems unnecessary and out of place.
> 8. There are grammar and punctuation errors scattered throughout; please edit carefully.
>
>
> a. Is the quality of the figures and tables satisfactory?
> - Not Applicable
>
> b. Does the reference list cover the relevant literature adequately and in an unbiased manner?
> - Yes
>
> c. Does this manuscript refer only to published data? (unpublished or original data is not allowed for this article type)
> - Yes
>
> d. Does the review include a balanced, comprehensive, and critical view of the research area?
> No answer given.
>
>
> ========
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> --
>
> Alexander Kulesza
>
> Team leader
>
> Modeling & simulation / Biomodeling
>
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>
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