[Vp-integration-subgroup] [EXT] Re: White paper revision
Tomas Helikar
thelikar2 at unl.edu
Tue May 18 07:08:25 PDT 2021
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 <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 9:05 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
> <mailto: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
>> <mailto: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
>> <mailto: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
>> theInternational 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> <mailto: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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