[Vp-integration-subgroup] White paper revision

Tue May 18 06:45:57 PDT 2021

Thanks John,

To clarify to all those who did not attend the meeting, the point people
list you provided was a compromise suggested by Sheriff so that there will
be no waste of time by making modifications that will not be accepted by
one of the contributors.

The summary of the meeting is available here:
https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-May/000138.html

To remind you, copyright transfer demands you get approval from all
contributors who participated in writing the manuscript. I was concerned
about the many deletions of material from many contributors at the
introduction. I do not believe those are necessary to maintain proper style
and in any case substance is more important than format. So we will need to
approve the manuscript with all contributors after edits are made. So we
are trying to locate the contributions of each person before you spend time
making edits that will not be approved. The idea is that you can more
easily collaborate with the contributors to smooth edits.

To locate the contributors, you need to go back to the original paper
versions and some contributors sent me their contributions by email and I
added them - so you may see my name as the author of the revision that
added the text - yet if you look at the references you removed it may give
you an indication of who contributed the text. I did this process once when
I merged the documents and it took many hours - I do not envy you so this
is why we are trying to locate who wrote what text to make it easier on you
to preserve all the substance of contributions.

I am still concerned about the introduction and references you deleted -
many people added material there. Yet to be practical, here are a few
comments that will be helpful:

1. I ask that to maintain continuity and keep all previous versions, people
will work on the original version -
https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
- I added you as an editor and several other people already have access - I
ask that you do not open for the public due security reasons - I can
privately show you examples of things that happened in the past when access
was granted.  If you want to work on the link you started, please maintain
continuity and put a link to all previous versions you are based on - after
all its a paper about reproducibility and maintaining a link to all
versions that document our process is in the spirit of reproducibility - it
also allows exploring who contributed what.

2. To make it easier on you I am demonstrating how someone else can help
you locate their text. Please add my name on
(2)  "The variety of modeling languages" - I have some text there I wish to
remain intact - so please all my name
(9) "Environments to adapt and integrate models" - you renamed that section
from Modeling requires adaptation towards integration and I have some text
there I want to remain intact - Also, since we are adding new
contributions, I will contribute some text about ensemble models that was
recently published.
(10) "Challenges for stochastic models" - I have some text there I wish to
remain intact - so please all my name

3. I remind you that we have contributors who want to add new text and
perhaps new sections - some already created alternative versions - so
please be mindful. Here are names I remember: Tingting Tang wants to add to
a section about data , Alexander Kulesza , Tomas Helikar , and Jim Sluka
wanted to contribute to the paper - Alexander has a version with changes.

I added James Faeder email to this discussion since I am not sure he is on
the mailing list - I recall adding his text manually. - yet I might be
wrong - it has been a long time.

I am writing this to avoid you wasting time on modifications that will face
objections. Hopefully this list will help.

            Jacob

On Tue, May 18, 2021 at 12:10 AM John Gennari <gennari at uw.edu> wrote:

>
> 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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