[Vp-reproduce-subgroup] [Vp-integration-subgroup] [EXT] Re: White paper revision

Tue May 18 07:05:12 PDT 2021

Yes Sheriff,

You have a good point. Here are the versions of the paper that I recall.

1. The version we all approved - I suggest we use this:
https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
2. John Gennari version:
https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?ts=60a294c2
3. Rahuman Sheriff version:
https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit
4. Alexander Kulesza version
https://drive.google.com/file/d/1U_lTHrV6STXWNT3GiCepvsLk1WdYgzN5/view
5. Original Model Reproducibility, Credibility, Standardization subgroup
version
https://docs.google.com/document/d/1cqwXAjBWEiJZ1tUBnf66QVHdHd2fKq_W0py7t4PNVLo/edit?usp=sharing
6. Original Integration subgroup  version:
https://docs.google.com/document/d/1voUSrSpv3AZlC1T-BLa3W4wzHQ5vEdJCVrBbwMUTDiQ/edit?usp=sharing

The last two versions hold the original discussions before the merge to the
version on top. The history of those contain most contributions - however
it will take hours to figure out where each text portion is located in the
new version. Yet the new version also includes many modifications. And I
believe Hana has another version of proofs that were never made public - we
did this revision and proof process before, yet I think she sent me her
version privately. I may be mistaken - it was a long time ago.

Hopefully this list will help understand the undertaking and save time.

             Jacob

On Tue, May 18, 2021 at 8:34 AM Rahuman Sheriff <sheriff at ebi.ac.uk> wrote:

> Dear John G,
> Many thanks for the update.
> I like the new ordering :)
>
> @Jacob, as you mentioned you have 6 versions, could you please add the
> link to those versions in  John G document, so they are all inked.
> I give consent to to rephrase my contribution or even remove part or all
> of my contribution to the white paper and present the ideas in other
> sections if required to make the paper coherent and flow well.
>
> The white paper has a great collections of ideas, I hope we can get it
> into a  good shape soon for submission and benefit the scientific community.
>
> Best regards
> Sheriff
>
>
> On 18 May 2021, at 13:28, James Osborne <jmosborne at unimelb.edu.au> wrote:
>
> Sorry I wasn't on the call Yesterday (it was 1 am for me so not really
> achievable). Looking at the emails looks like it was useful.
>
> Happy to help how I can, in terms of areas as someone on the multicellular
> side of life i'm probably most use on 3 but happy to support others.
>
> James
>
> On Tue, May 18, 2021 at 3:12 PM John Gennari <gennari at uw.edu> wrote:
>
>> * External email: Please exercise caution *
>> ------------------------------
>>
>>
>> All: About 9 of us had a lively Zoom meeting today to chat about the
>> manuscript. By the end, it was a productive meeting, and I'm hoping that
>> this email will capture some key outputs from the meeting. I apologize if I
>> said some things that were a bit "inflammatory". Obviously 2 years would be
>> much too long to get this paper out-the door.
>>
>> I saw two outcomes. First, we had some nice ideas and discussion about
>> re-ordering (initiated by Tomas Helikar). In the below, I'm going to
>> propose one possible ordering, but this is certainly a work-in-progress.
>> The reason that I think ordering is important is that it will give us a
>> much better ability to write a strong concluding section, where we talk
>> about themes and the larger arc of our ideas.
>>
>> Second, we agreed that we should nominate "point persons" who would be in
>> charge of at least the initial cut of each of the subsections. As Jacob
>> pointed out, this information should be easy to get from older email and
>> history of the development of the paper. During the zoom meeting, we
>> associated some co-authors with some sections, but our coverage wasn't
>> perfect (see challenge #12). Hopefully people will "stand up" and admit
>> that some section of text is theirs.
>>
>> So in the below, I include the original title of the section, a few words
>> about the content of that section, and then a name (or several names) of
>> co-authors who will be the "point person" to make sure that the appropriate
>> content is included. Obviously, all co-authors can and should chime in on
>> any part of the text, but the point person should make sure that the key
>> ideas are included.
>>
>> The basic ordering idea for the dozen challenges was to follow the
>> life-cycle of model development, execution, sharing and integration, and
>> eventually implementation. So...
>>
>> *********************************************
>>
>> *(1) "**Data** and measurement definitions*". Before you can build a
>> model, you must have data. So data availability and measurement standards
>> is the place to start.
>>
>> *People: *Hana D, Jacob B
>>
>> *(2) "**The variety of modeling languages*" This is about the choice of
>> modeling languages, such as using SBML, CellML, or Matlab. As I said on the
>> phone call, this is sort of about "syntax"--how do you write down your
>> model?
>>
>> *People:* John G, Jon K, Rahuman S.
>>
>> *(3) "**The variety of modeling paradigms and scales"* Separately from
>> modeling syntax, we must acknowledge modeling paradigms with very different
>> semantics. Some clear examples are PDEs versus ODEs versus rule-based
>> systems (and obviously one can combine these). Certainly semantics might
>> impact syntax (the prior challenge), in that certain modeling language
>> might be appropriate only for some paradigms.
>>
>> People: James G, Eric F (?)
>>
>> *(4) "**Units standardization*" A common reason that models are not
>> reproducible are errors in units, or misunderstanding about units, or
>> simply a lack of information about units.
>>
>> People: Jacob B, Hana D
>>
>> *(5) "**A lack of annotations in models*". Once researchers publish
>> models, they must annotate the model so that others can understand it.
>> Quality annotation is essential for both search and reproducibility.
>>
>> People: John G.
>>
>> *(6) "**Models are hard to locate"* If your goal is to reproduce,
>> understand and possibly reuse or integrate some other model, one must first
>> find that model. This requires annotation (prior section) and repositories
>> (Physiome Model Repository, BioModels) and search platforms
>> (ModeleXchange).
>>
>> People: Jon K, John G.
>>
>> *(7) "**Common platforms to execute models" *A model is pretty worthless
>> as a static object. For folk to understand and reproduce models they must
>> be executable. Alas, there is no single or consistent way of executing a
>> model -- and of course, this interacts direction with section #2 and #3,
>> above: Execution platforms are usually only for one modeling paradigm, and
>> often for one modeling language. The BioSimulators work goes here.
>>
>> People: Jon K.
>>
>> *(8) "**Credibility **and validity of models*" Once a model is
>> published, how do folk know it is right? Model validation is a big topic
>> and challenge. Credibility follows (in part) from validation, but also
>> requires transparency and reproducibility, etc.
>>
>> People: John Rice, Jon K, Jacob B
>>
>> *(9) "**Environments to adapt and integrate models*" As I see it, one of
>> the end-targets for this manuscript is to better enable model integration,
>> to build better models. There are many challenges with the task of
>> integrating two (or more) models. (One that has recently been discussed is
>> that even if model A and model B are valid and correct, there is no
>> guarantee that the combined model A+B is correct. I liked what William
>> Waites and Katherine Morse posted on this subject.) This section is where
>> SBML-comp and SemGen environments can be mentioned.
>>
>> People: John G.
>>
>> (*10) "Challenges for stochastic models" *Special challenges specific to
>> stochaistic modeling. An obvious point to mention is repeatability --
>> stochastic models don't necessarily give the same results with the same
>> inputs.
>>
>> People: James G., Eric F
>>
>> *(11) "Licensing barriers" *Issues around "open source" and CC0
>> licensing.
>>
>> People: Jacob B
>>
>> *(12) "Barriers to model implementations and applications"*  (I might
>> suggest this be re-phrased for better clarity). What this section should
>> discuss are challenges is getting a community to actually use models for
>> "real-world" applications or decision making. This is more of a
>> cultural/societal challenge, and thus seems like a nice big-picture way to
>> end.
>>
>> *People: ?? *I don't have any names here...
>>
>> *********************************************
>>
>> We didn't really talk much about it in the Zoom meeting, but there have
>> been ideas tossed around about a "baker's dozen", i.e., adding a 13th
>> challenge. We could also potentially merge some of the above.
>>
>> The "point persons" listed above is obviously a subset of co-authors.
>> That's fine and appropriate. Just for transparency, I follow what I think
>> is pretty standard policy for authorship issues, and nicely summarized by
>> the International Committee of Medical Journal Editors (ICMJE); see 2019
>> updated document at http://www.icmje.org/icmje-recommendations.pdf  (Or
>> see, below my signature, a summary of the key points of this document).
>>
>> Finally, I've made the document editable by all at
>> https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?ts=60a294c2
>>
>> -John G.
>> ==========================================================================
>> Associate Professor & Graduate Program Director      <gennari at uw.edu>
>> <gennari at uw.edu>
>> Dep't of Biomedical Informatics and
>> telephone:206-616-6641
>>     Medical Education, box 358047
>> University of Washington
>> Seattle, WA  98109-4714
>> http://faculty.washington.edu/gennari/
>> ==========================================================================
>>
>>
>> The ICMJE recommends that authorship be based on the following 4
>> criteria:
>>
>> 1.      Substantial contributions to the conception or design of the
>> work; or the acquisition, analysis, or interpretation of data for the work;
>> AND
>>
>> 2.      Drafting the work or revising it critically for important
>> intellectual content; AND
>>
>> 3.      Final approval of the version to be published; AND
>>
>> 4.      Agreement to be accountable for all aspects of the work in
>> ensuring that questions related to the accuracy or integrity of any part of
>> the work are appropriately investigated and resolved.
>>
>>
>>
>>
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