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

Tue May 18 07:53:53 PDT 2021

I was in a Msc defence yesterday so I couldn't make it to the zoom meeting.
I can help with item (*8) "**Credibility **and validity of models*"  and
since nobody is in  *(12) "Barriers to model implementations and
applications"  *I can start contributing there too.

Best,

***************************************************************************
Gilberto C. Gonzalez-Parra, Ph.D in Applied Mathematics.
Faculty of the Mathematics Department
New Mexico Tech, NM, USA.
****************************************************************************

On Tue, May 18, 2021 at 8:30 AM Tomas Helikar <thelikar2 at unl.edu> wrote:

> Since John is taking the lead on the new version, my suggestion is to let
> him do it the way that will be most efficient for him. I think everyone,
> including John, have noted your concerns.
> Tomas Helikar, Ph.D.
> Susan J. Rosowski Associate Professor
> Department of Biochemistry | University of Nebraska-Lincoln
> m: 402-547-8904 <callto:402-547-8904> | o: 402-472-3530
> <callto:402-472-3530>
> www.helikarlab.org <http://www.postbox-inc.com> | cellcollective.org
> <http://helikarlab.org>
> twitter: @helikarlab <http://twitter.com/helikarlab>, @biocollective
> <http://twitter.com/biocollective>
> On 5/18/21 9:27 AM, Jacob Barhak wrote:
>
> Non-NU Email
> ------------------------------
> So Tomas,
>
> Before starting editing, to save time it is important that we establish
> what is going to be edited - I voiced my concern over the large deletions
> in Johns version more than once - there is a real problem there - many
> authors may be completely eliminated in the name of style - I don't like it
> - so John has to decide how he spends his time - first just define what
> sections you want to contribute in - this will help John comprehend the
> magnitude of the task - he promised editorial services for two weeks - so
> before we start wasting time with edits, lets see the entire picture.
>
> Tomas, what you like may be something I dislike or something I do not care
> about, and eventually we all have to agree - and there are about 20 of us -
> this is a legal requirement for copyright transfer. The task here is time
> consuming and I do not envy John and it is important we all help him
> realize the task before he spends time on it.
>
> And please reply to all - there are some contributors that are listed in
> only one list and some that may not have signed up - they all need to be
> aware of what we are doing.
>
> Hopefully you identified the sections you want to contribute to - please
> state those to move this forward quicker.
>
>             Jacob
>
>
>
> On Tue, May 18, 2021 at 9:08 AM Tomas Helikar <thelikar2 at unl.edu> wrote:
>
>> I suggest we use John's version - the flow has begun to improve there and
>> he'll be bringing the content over from the submitted version.
>>
>> At the top of each of the other version, there should be big red "DO NOT
>> EDIT THIS VERSION" and a link to John's version that will be the running
>> draft where our efforts should focus.
>>
>> Best,
>> Tomas Helikar, Ph.D.
>> Susan J. Rosowski Associate Professor
>> Department of Biochemistry | University of Nebraska-Lincoln
>> m: 402-547-8904 <callto:402-547-8904> | o: 402-472-3530
>> <callto:402-472-3530>
>> www.helikarlab.org
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.postbox-2Dinc.com&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=8pX0Br54uLoNQ-PxHY_Nt9ks6sIqSjFiajTJf6yTLYE&s=hJenfL7Oc5LHMtfzjwCDD7iz11gFb7qHTa9Hbu2i1Lk&e=>
>> | cellcollective.org
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__helikarlab.org&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=8pX0Br54uLoNQ-PxHY_Nt9ks6sIqSjFiajTJf6yTLYE&s=sM2xjtRiGe7zBH5cWvHqEuH6DqVSiUxQjrE9DZ6JJVI&e=>
>> twitter: @helikarlab
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_helikarlab&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=8pX0Br54uLoNQ-PxHY_Nt9ks6sIqSjFiajTJf6yTLYE&s=bdp23tv-IbXxRa2YpzF18AkQutpCxDtfC7-siSRd5io&e=>,
>> @biocollective
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_biocollective&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=8pX0Br54uLoNQ-PxHY_Nt9ks6sIqSjFiajTJf6yTLYE&s=WcTsfij98jsXskRk-5qag6ax8_-PZrtIZ5o5R_QV-VQ&e=>
>> On 5/18/21 9:05 AM, Jacob Barhak wrote:
>>
>> Non-NU Email
>> ------------------------------
>> 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
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1IMEgmdNkx-2DEsnOjGuegpenSIMmKIkK00Lc8Gred3QxM_edit-3Fusp-3Dsharing&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=FanQUPp95Lqx2G9Ojb6SLVQzkZS6mrqBIt_W-zgW8_Q&e=>
>> 2. John Gennari version:
>> https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?ts=60a294c2
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1VvyP3YZQdQYjj8DFKOpQ4pn-5F0pdDGgiT_edit-3Fts-3D60a294c2&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=7h_7qlaNYzcnYViiFjrrVhBADdtnSQ8eh_Wg_vxmY4I&e=>
>> 3. Rahuman Sheriff version:
>> https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh_edit&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=yaBZO6lyEXDKmMXfrDPDqy10sDgl0FQgkFFMO3_iShg&e=>
>> 4. Alexander Kulesza version
>> https://drive.google.com/file/d/1U_lTHrV6STXWNT3GiCepvsLk1WdYgzN5/view
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1U-5FlTHrV6STXWNT3GiCepvsLk1WdYgzN5_view&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=6gQoAQCH7F2WOy92A0xjfWmCMUjW7onPku8BYcIsY9Y&e=>
>> 5. Original Model Reproducibility, Credibility, Standardization subgroup
>> version
>> https://docs.google.com/document/d/1cqwXAjBWEiJZ1tUBnf66QVHdHd2fKq_W0py7t4PNVLo/edit?usp=sharing
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1cqwXAjBWEiJZ1tUBnf66QVHdHd2fKq-5FW0py7t4PNVLo_edit-3Fusp-3Dsharing&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=QH6Rgy4why7ib2YGE2T5AA61L68xDE1K-ySoCdKV9ew&e=>
>> 6. Original Integration subgroup  version:
>> https://docs.google.com/document/d/1voUSrSpv3AZlC1T-BLa3W4wzHQ5vEdJCVrBbwMUTDiQ/edit?usp=sharing
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1voUSrSpv3AZlC1T-2DBLa3W4wzHQ5vEdJCVrBbwMUTDiQ_edit-3Fusp-3Dsharing&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=WPFW1D-ECFULPKl8uijQsNA58J5V7TNynIc9OeqCiBE&e=>
>>
>> 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
>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.icmje.org_icmje-2Drecommendations.pdf&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=l29d3A9PItAUv4N0WkCuREqes9tSKSW7sk5GDEo6VBA&e=>
>>>> (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
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1VvyP3YZQdQYjj8DFKOpQ4pn-5F0pdDGgiT_edit-3Fts-3D60a294c2&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=7h_7qlaNYzcnYViiFjrrVhBADdtnSQ8eh_Wg_vxmY4I&e=>
>>>>
>>>> -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/
>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__faculty.washington.edu_gennari_&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=7h8T10a2oOTChEmXp5dGxDnAIghmjMroKsXSfcbIH9Y&e=>
>>>>
>>>> ==========================================================================
>>>>
>>>>
>>>> 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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>>>
>>
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