[Vp-reproduce-subgroup] Paper review and revision check list
Alexander Kulesza
alexander.kulesza at novadiscovery.com
Mon Dec 20 13:50:32 PST 2021
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:
>
>
> 1. We should discuss the references that reviewer 1 raised and add
> them as reference
> 2. 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?
> 3. 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
> 4. Reviewer 1 asked for additional graphics - I am unsure how to
> address this beyond ur current diagram - ideas will help
> 5. 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.
> 6. 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
> 7. 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.
> 8. 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.
> 9. 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.
> 10. 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.
> 11. 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.
> 12. 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."
> 13. 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
>
>
>
>
>
>
> -
>
>
>
>
>
> ########### 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
alexander.kulesza at novadiscovery.com
+33 7 82 92 44 62
nova
DISCOVERY
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